1,288
Views
114
CrossRef citations to date
0
Altmetric
Research Article

Protein Structure Prediction: Recognition of Primary, Secondary, and Tertiary Structural Features from Amino Acid Sequence

, &
Pages 1-94 | Published online: 26 Sep 2008

References

  • Abagyan R., Frishman D. I., Argos P. Recognition of distantly related proteins through energy calculations. Proteins 1994a; 19: 132–140
  • Abagyan R., Totrov M., Kuznetsov M. ICM—a new method for protein modeling and design: applications to docking and sttuctun prediction from the distorted native conformation. J. Comp. Chem. 1994b; 15: 488–506
  • Abagyan R., Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 1994; 235: 983–1002
  • Abagyan R. A. Towards protein folding by global energy optimization. FEBS Lett. 1993; 325: 17–22
  • Abagyan R. A., Argos P. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 1992; 225: 519–532
  • Abagyan R. A., Maiorov V. N. A simple quantitative representation of polypeptide chain folds: comparison of protein tertiary structures. J. Biomol. Struct. Dyn. 1988; 5: 1267–1279
  • Abagyan R. A., Maiorov V. N. An automatic search for similar spacial arrangements of alfa-helices and beta-strands in globular proteins. J. Biomol. Struct. Dyn. 1989; 6: 1045–1059
  • Abola E. E., Bemstein F. C., Bryant S. H., Koetzle T. F., Weng J., Allen F. H., Bergerhoff G., Sievers R. Crystallographic databases—information content, software systems, scientific applications. Chester Data Commission of the International Union of Crystallography, Bonn, Cambridge 1987; 107–132, Protein data bank
  • Adzhubei A. A., Stemberg M. J. E. Left-handed polyproline II helices commonly occur in globular proteins. J. Mol. Biol. 1993; 229: 472–493
  • Aleman C., Oroczo M. On the suitability of semiempirical calculations as sources of force field parameters. J. Comp.-Aid. Mol. Des. 1992; 6: 3311–3348
  • Alexandrov N. N., Takahashi K., Go N. Common spacial arrangements of backbone fargments in homologous and non-homologous proteins. J. Mol. Biol. 1992; 225: 5–9
  • Alexandrov N. N., Go N. Biological meaning, statistical significance, and classification of local spatial similarities in non-homologous proteins. Prot. Sci. 1994; 3: 866–875
  • Anfinsen C. B. Principles that govern the folding of protein chains. Science 1973; 181: 223–230
  • Argos P. Analysis of sequence similar pentapep-tides in unrelated protein tertiary structures. J. Mol. Biol. 1987; 197: 331–348
  • Argos P. Sensitive methods for determining the relatedness of proteins with limited sequence homology. Curr. Opin. Biotech. 1994; 5: 361–371
  • Arnold G. E., Dunker K., Johns S. J., Douthart R. J. Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure. Proteins 1992; 12: 382–399
  • Aronson H.-E. G., Royer W. E., Jr., Hendrickson W. A. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold. Prot. Sci. 1994; 3: 1706–1711
  • Aszodi A., Taylor W. R. Folding polypep-tide α-carbon backbones by distance geometry methods. Biopolymers 1994; 34: 489–505
  • Attwood T. K., Beck M. E. PRINTS—a protein motif fingerprint database. Prot. Eng. 1994; 7: 841–848
  • Bachar O., Fischer D., Nussinov R., Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Prot. Eng. 1993; 6: 279–288
  • Bairoch A. The Prosite dictionary of sites and patterns in proteins, its current status. Nucl. Acid Res. 1993; 21: 3097–3103
  • Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank, recent developments. Nucl. Acid Res. 1993; 21: 3093–3096
  • Baker D., Sohl J. L., Agard D. A. A protein-folding reaction under kinetic control. Nature 1992a; 356: 263–265
  • Baker D., Sohl J. L., Agard D. A. Protease Pro region required for folding is a potent inhibitor of the mature enzyme. Proteins 1992b; 12: 339–344
  • Barnes E. J., Hut P. Error analysis of a tree code. Astrophys. J. Suppl. Ser. 1989; 70: 389–417
  • Barre S., Greenberg A. S., Flajnik M. K., Chothia C. Structural conservation of hypervariable regions in immunoglobins evolution. Nature Struct. Biol. 1994; 1: 915–920
  • Barton G. J., Stemberg M. J. E. LOPAL and SCAMP: techniques for the comparison and display of protein structures. J. Mol. Graph. 1988; 6: 190–196
  • Bascle J., Garel T., Orland H., Velikson B. Biasing a Monte Carlo chain growth method with Ramachandran's plot: application to twenty-L-alanine. Biopolymers 1993; 33: 1843–1849
  • Bassolino-Klimas D., Bruccoleri R. E. Application of a directed conformational search for generating 3-D coordinates for protein structures from acarbon coordinates. Proteins 1992; 14: 465–474
  • Bauer A., Beyer A. An improved pair potential to recognize native protein folds. Proteins 1994; 18: 254–261
  • Baumann G., Frömmel C., Sander C. Polarity as criterion in protein design. Prot. Eng. 1989; 2: 329–324
  • Beglov D. B., Lipanov A. A. Charge grouping approaches to calculation of electrostatic forces in molecular dynamics of proteins. J. Biomol. Struct. Dyn. 1991; 9: 205–214
  • Bell L. H., Coggins J. R., Miher-White E. J. Mix‘n’Match: an improved multiple sequence alignment procedure for distantly related proteins using secondary structure predictions, designed to be independent of the choice of gap penalty and scoring matrix. Prot. Eng. 1993; 7: 683–690
  • Bemstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. Protein data bank. a computer based archival file for macromolecular structures. J. Mol. Biol. 1977; 112: 535–542
  • Beveridge D. L., DiCapua F. M. Free energy via molecular simulation. Ann. Rev. Biophys. Biophys. Chem. 1989; 18: 431–492
  • Biou V., Gibrat J. F., Lervin J. M., Robson B., Gamier J. Secondary structure prediction: combination of three different methods. Prot. Eng. 1988; 2: 185–191
  • Blaber M., Zhang X.-J., Matthews B. W. Structural basis of amino acid alpha helix propensities. Science 1993; 269: 1637–1640
  • Blaber M., Zhang X.-J., Lindstrom J. L., Pepiot S. D., Baase W. A., Matthews B. W. Determination of alpha-helix propensities within the context of a folded protein: sites 44 and 131 in bacteriophage T4 lysozyme. J. Mol. Biol. 1994; 235: 600–624
  • Bohr H., Bohr J., Brunak S., Cotterill R. M. J., Fredholm H., Lautrup B., Petersen S. B. A novel approach to the prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Lett. 1990; 261: 434
  • Bohr J., Bohr H., Bmak S., Cotterill R. M. J., Fredholm H., Lautrup B., Petersen S. B. Protein structures from distance inequalities. J. Mol. Biol. 1993; 231: 861–869
  • Borchert T. V., Abagyan R., Rahda Kishan K. V., Zeelen J. P., Wierenga R. K. The crystal structure of an engineered triose-phosphate isomerase, monoTIM: the correct modeling of an eight-residue loop. Structure 1993; 1: 205–213
  • Bork P. Mobile modules and motifs. Curr. Opin. Struct. Biol. 1992; 2: 413–421
  • Bork P., Sander C., Valencia A. An AT-Pase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 7290–7294
  • Bork P., Preissner R. On α-helices terminated by glycine. II. Recognition by sequence pattern. Biophys. Biochem. Res. Comm. 1991; 180: 666–672
  • Bouzida D., Kumar S., Swendson R. H. Efficient Monte Car 10 methods for computer simulation of biological molecules. Phys. Rev. A 1992; 45: 8894–8901
  • Bowie J. U., Clarke N. D., Pabo C. O., Sauer R. T. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins 1990; 7: 257–264
  • Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional stricture. Science 1991; 253: 164–170
  • Braakman I., Helenius J., Helenius A. Role of ATP and disulfde bonds during protein folding in the endoplasmic reticulum. Nuture 1992; 356: 260–262
  • Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 1983; 4: 187–217
  • Brown W. J., North A. C. T., Phillips D. C., Brew K., Vanaman T. C., Hill R. L. A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol. 1969; 42: 65–86
  • Bruccoleri R. E. Application of systematic con-formational search to protein modeling. Mol. Simul. 1993; 10: 151–174
  • Brünger A. T., Karplus M. Molecular dynamics simulation with experimental restraints. Acc. Chem. Res. 1991; 24: 54–61
  • Bryant S. H., Lawrence C. E. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993; 16: 92–112
  • Busetta B. The use of folding patterns in the search of protein structural similarities: a three-dimensional model of phosphoribosyl transferases. Biochim. Biophys. Acta. 1988; 957: 21–33
  • Busetta B., Barrans Y. The prediction of protein topologies. Biochim. Biophys. Acta. 1982; 709: 73–83
  • Busetta B., Barrans Y. The prediction of protein domains. Biochim. Biophys. Acta. 1984; 790: 117–124
  • Bussian B. M., Sander C. How to determine protein secondary structure in solution by Raman spectroscopy: practical guide and test case DNase I. Biochemistry 1989; 28: 4271–4277
  • Byme D., Li J., Platt E., Robson B., Weiner P. K. Novel algorithms for searching confor-mational space. J. Comp.-Aid. Mol. Des. 1994; 8: 67–82
  • Casari G., Beyer A. 1994, personal communication
  • Casari G., Sippl M. J. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins are able to identify native folds. J. Mol. Biol. 1992; 224: 725–732
  • Chelvanayagam G., Roy G., Argos P. Easy adaptation of protein structure to sequence. Prot. Eng. 1994; 7: 173–184
  • Chothia C. One thousand families for the molecular biologist. Nature 1992; 357: 543–544
  • Chothia C., Ltsk A. M. The relation between the divergence of sequence and struchue in proteins. EMBO J. 1986; 5: 823–826
  • Chou K.-C., Zhang C.-T. A correlation-coefficient method to predicting protein-structural classes from amino acid composition. Eur. J. Biochem. 1992; 207: 429–433
  • Chou K.-C., Zhang C.-T. A new approach to prediction protein folding types. J. Prot. Chem. 1993; 12: 169–178
  • Chou P. Y. Prediction of protein structural classes from amino acid composition. Prediction of protein structure, G. D. Fasman. Plenum Press, New York 1989; 549–586
  • Chou P. Y., Fasman G. Prediction of protein conformation. Biochemistry 1974a; 13: 222–245
  • Chou P. Y., Fasman G. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974b; 13: 211–222
  • Chou P. Y., Fasman G. Prediction of secondary structure of proteins from their amino acid sequence. Adv. Enrymol. 1978; 47: 145–147
  • Chou P. Y., Zhang C.-T. A joint prediction of the folding types of 1490 human proteins from their genetic codons. J. Theor. Biol. 1993; 161: 251–262
  • Claessens M., Van Cutsem E., Lasters I., Wodak S. J. Modeling the polypeptide backbone with 'spare parts' from known protein structures. Prot. Eng. 1989; 2: 335–345
  • Claverie J.-M. Database of ancient sequences. Nature 1993; 364: 19–20
  • Cohen B. I., Presnell S. R., Cohen F. E. Pattern-based approaches to protein structure prediction. Methods in Enzymology, J. J. Langone. Academic Press, San Diego 1991; Vol. 202: 252–268
  • Cohen B. I., Presnell S. R., Cohen F. E. Origins of structural diversity within sequentially identical hexapeptides. Prot. Sci. 1993; 2: 2134–2145
  • Cohen F. E., Abarbanel I. D., Kuntz I. D., Fletterick R. J. Turn prediction in proteins using a pattern matching approach. Biochemistry 1986; 25: 266–215
  • Cohen F. E., Sternberg M. J. E. On the prediction of protein structure: the significance of the root-mean-square deviation. J. Mol. Biol. 1980; 138: 321–333
  • Colloc'h N., Etchebest C., Thoreau E., Henrissat B., Momon J.-P. Comparison of three algorithms for the assignment of secondary structure in proteins: the advantage of a consensus assignment. Prot. Eng. 1993; 6: 377–382
  • Collura V., Higo J., Gamier J. Modeling of proteins loops by simulated annealing. Prot. Sci. 1993; 2: 1502–1510
  • Colovos C., Yeates T. O. Verification of protein structures: patterns of nonbonded atomic interactions. Prot. Sci. 1993; 2: 1511–1519
  • Correa P. E. The building of protein structures from α-carbon coordinates. Proteins 1990; 7: 366–377
  • Cramer C. J., Truhlar D. G. An SCF solvation model for the hydrophobic effect and absolute free energies of aqueous solvation. Science 1992; 256: 213–217
  • Creamer T. P., Rose G. D. Side-chain entropy opposes α-helix formation but rationalizes experimenbtally determined helix-forming propensities. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5937–5941
  • Creamer T. P., Rose G. D. α-helix-forming propensities in peptides and proteins. Proteins 1994; 19: 85–97
  • Creighton T. E. Protein Folding. Freeman, New York 1992
  • Crippen G. M. Prediction of protein folding from amino acid sequence over discrete conformation spaces. Biochemistry 1991; 30: 4232–4236
  • Crippen G. M., Snow M. A 1.8–Å resolution potential function for protein folding. Biopoly-mers 1990; 29: 1479–1489
  • Crippen G. M., Viswanadhan V. N. Sidechain and backbone potential function for conformational analysis of proteins. Int. J. Peptide Prot. Res. 1985; 25: 487–509
  • Dandekar T., Argos P. Potential of genetic algorithms in protein folding and protein engineering simulations. Prot. Ens. 1992; 5: 637–645
  • Dadekar T., Argos P. Folding the main chain of small proteins with the genetic algorithm. J. Mol. Biol. 1994; 236: 844–861
  • Dauber-Osguthorpe P., Roberts V. A., Osgu-Thorpe D. J., Wolff J., Genest M., Hagler A. T. Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins 1988; 4: 31–47
  • Dauber-Osguthorpe P., Osguthorpe D. J. Partitioning the motion in molecular dynamics simulations into characteristic modes of motion. J. Comp. Chem. 1993; 14: 1259–1271
  • David C. W. Sprouting side chain conformations in X-PLOR simulations of peptides. J. Comp. Chem. 1993; 14: 715–717
  • David C. W. Hydrating peptides using a sprouting technique. J. Comp. Chem. 1994; 15: 23–27
  • Davis M. E. The inducible multipole solvation model: a new model for solvation effects on solute electrostatics. J. Chem. Phys. 1994; 100: 5149–5159
  • Davis M. E., McCammon J. A. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 1990; 90: 509–521
  • De Fillipis V., Sander C., Vriend G. Redicting local structural changes that result from point mutations. Prot. Eng. 1994; 7: 1203–1208
  • Degli Eposti M., Crimi M., Venturoli G. A critical evaluation of the hydropathy profile of membrane proteins. Eur. J. Biochem. 1990; 190: 207–219
  • Deisenhofer J., Michel H. The photosyn-thetic reaction centre from the purple bacterium Rhodopseudomonas viridis. EMBO J. 1989; 8: 2149–2170
  • Desmet J., De Maeyer M., Hazes B., Lasters I. The dead-end elimination theorem and its use in side-chain positioning. Nature 1992; 356: 539–542
  • Diamond R. On the multiple simultaneous superposition of molecular structures by rigid body superposition. Prot. Sci. 1992; 1: 1279–1287
  • Ding H.-Q., Karasawa N., Goddard W. A. III, Atomic level simulations on a million particles: the cell multipole method for Coulomb and London interactions. J. Chem. Phys. 1992; 97: 4309–4315
  • Donelly D., Overington J. P., Blundell T. L. The prediction and orientation of α-helices from sequence alignments: the combined use of environmentdependent substitution tables, Fourier transform methods and helix capping rules. Prot. Eng. 1994; 7: 645–653
  • Doolittle R. F. Similar amino acid sequences: chance or common ancestry. Science 1981; 214: 149–159
  • Doolittle R. F. Counting and discounting the universe of exons. Science 1991; 253: 677–679
  • Dorit R. L., Schoenbach L., Gilbert W. How big is the universe of exons. Science 1990; 250: 1377–1381
  • Dorit R. L., Schoenbach L., Gilbert W., Reply to Doolittle R. F., Patthy L. Science 1991; 253: 679–680
  • Dorofeev V. E., Mazur A. K. Investigation of conformational equilibrium of polypep-tides by internal coordinate stochastic dynamics. Met5-enkephalin. J. Biomol. Struct. Dyn. 1993; 10: 143–167
  • Drexler K. E. Molecular engineering: an approach to the development of general capabilities for molecular manipulation. Proc. Natl. Acad. Sci. U. S. A. 1981; 78: 5275–5278
  • Dubchak I., Holbrook S. R., Kim S.-H. Prediction of protein folding class from amino acid composition. Proteins 1993; 16: 79–91
  • Dunbrack R. L., Karplus M. Backbone-dependent rotamer library for proteins. Application to sidechain prediction. J. Mol. Biol. 1993; 230: 543–574
  • Dunbrack R. L., Karplus M. Conformational analysis of the backbonedependent rotamer preferences of proteins sidechains. Nature Struct. Biol. 1994; 1: 336340
  • Dunfield L. G., Burgess A. W., Scheraga H. A. Energy parameters in polypeptides. VIII. Empirical potential energy algorithm for the conformational analysis of large molecules. J. Phys. Chem. 1978; 82: 2609–2616
  • Efimov A. V. Favoured structural motifs in globular proteins. Structure 1994; 2: 999–1002
  • Eisenberg D., Bowie J. U., Lüthy R., Choe S. Three-dimensional Protdes for analysing protein sequence-structure relationships. Farad. Disc. 1992; 93: 25–34
  • Eisenberg D., McLachlan A. D. Solvation energy in protein folding and binding. Nature 1986; 319: 199–203
  • Eisenhaber F., Lijnzaad P., Argos P., Sander C., Scharf M. The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and for generating dot surfaces of molecular assemblies. J. Comp. Chem. 1995; 16: 273–284
  • Eisenhaber F., Argos P. Improved strategy in analytic surface calculation for molecular systems: handling of singularities and computational efficiency. J. Comp. Chem. 1993; 14: 1272–1280
  • Eisenmenger F., Argos P., Abagyan R. A. A method to configure protein sidechains from the mainchain trace in homology modeling. J. Mol. Biol. 1993; 231: 849–860
  • Elofsson A., Nilsson L. How consistent are molecular dynamics simulations. J. Mol. Biol. 1993; 233: 766–780
  • Evans D. J., Murad S. Singularity free algorithm for molecular dynamics simulation of rigid polyatomics. Mol. Phys. 1977; 34: 327–331
  • Factor A. D., Mehler E. L. Graphical representation of hydrogen bonding patterns in proteins. Prot. Eng. 1991; 4: 421–425
  • Fetrow J. S., Bryant S. H. New programs for protein tertiary structure prediction. Biorechnology 1993; 11: 479–484
  • Fincham D. Leapfrog rotational algorithms for linear molecules. Mol. Simul. 1993; 11: 79–89
  • Finkelstein A. V., Janin J. The price of lost freedom: entropy of bimolecular complex formation. Prot. Eng. 1989; 3: 1–3
  • Finkelstein A. V., Reva B. A search for the most stable folds of protein chains. Nature 1991; 351: 497499
  • Flores T. P., Orengo C. A., Moss D. S., Thornton J. M. Comparison of conformational characteristics in structurally similar protein pairs. Prot. Sci. 1993; 2: 1811–1826
  • Fraenkel A. S. Complexity of protein folding. Bull. Math. Biol. 1993; 55: 1199–1210
  • Friedman H. L. Image approximation to the reaction field. Mol. Phys. 1975; 29: 1533–1543
  • Frishman D. I., Argos P. Recognition of distantly related protein sequences using conserved motifs and neural networks. J. Mol. Biol. 1992; 228: 951–962
  • Frömmel C. Use of averaged mutation rate in pieces of protein sequences to predict the location of antigenic determinations. J. Theor. Biol. 1988; 132: 171–177
  • Furois-Corbin S., Smith J. C., Kneller G. R. Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin. Proteins 1993; 16: 141–154
  • Gamier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 1978; 120: 97–120
  • Gamier J., Levin J. M. The protein structure code: what is its present status. Comput. Appl. Biosci. 1991; 7: 133–142
  • Genfa Z., Xinhua X., Zhang C.-T. A weighting method for prediction of protein structural class from amino acid composition. Eur. J. Biochem. 1992; 210: 747–749
  • Geourjon C., Deléage G. SOPM: a self-optimized method for protein secondary structure prediction. Prot. Eng. 1994; 7: 157–164
  • Gerber P. Peptide mechanics: a force field for peptides and proteins working with entire residues as smallest units. Biopolymers 1992; 32: 1003–1017
  • Gething M. J., Sambrook J. Protein folding in the cell. Nature 1992; 355: 3345
  • Gibrat J.-F., Gamier J., Robson B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol. 1987; 198: 42543
  • Gibrat J.-F., Robson B., Gamier J. Influence of the local amino acid sequence upon the zones of the torsional angles phi and psi adopted by residues in proteins. Biochemistry 1991; 30: 1578–1586
  • Gibson K. D., Scheraga H. A. Decisions in force field development. Reply to Kollman and Dill. J. Biomol. Struct. Dyn. 1991; 8: 1109–1111
  • Gibson T. J., Thompson J. D., Abagyan R. A. Proposed structure for the DNA-binding domain of the Helix-Loop-Helix family of eucaryotic gene regulatory proteins. Prot. Eng. 1993; 6: 41–50
  • Gibson T. J., Hyvönen M., Musacchio A., Saraste M., Birney E. PH domain: the first anniversary. Trends Biochem. Sci. 1994; 19: 349–353
  • Godzik A., Kolinski A., Skolnick I. Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 1992; 227: 227–238
  • Godzik A., Kolinski A., Skolnick J. Lattice representations of globular proteins: How good are they. J. Comp. Chem. 1993; 14: 1194–1202
  • Godzik A., Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 12098–12102
  • Goldstein R., Luthey-Schulten Z. A., Wolynes P. G. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. U. S. A. 1992a; 89: 4918–4922
  • Goldstein R., Luthey-Schulten Z. A., Wolynes P. G. Protein tertiary structure recognition using optimized hamiltonians with local interactions. Proc. Natl. Acad. Sci. U. S. A. 1992b; 89: 9029–9033
  • Goldstein R. F. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys. J. 1994; 66: 1335–1340
  • Gracy J., Chiche L., Sallantin J. Improved alignment of weakly homologous protein sequences using structural information. Prot. Eng. 1993; 6: 821–829
  • Green P., Lipman D., Hillier L., Waterstone R., States D., Claverie J.-M. Ancient conserved regions in new gene sequences and in the protein databases. Science 1993; 259: 1711–1715
  • Greengard L. Fast algorithms for classical physics. Science 1994; 265: 909–914
  • Greer J. Comparative model-building of the mammalian serine proteases. J. Mol. Biol. 1981; 153: 1027–1042
  • Gregoret L. M., Cohen F. E. Novel method for the rapid evaluation of packing in protein structures. J. Mol. Biol. 1990; 211: 959–974
  • Gribskov M., McLachlan A. D., Eisenberg D. Protile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. U. S. A. 1987; 84: 4355–4358
  • Gribskov M., Uthy L. R., Eisenberg D. Protile analysis. Methods Enzymol. 1990; 183: 16–159
  • Grindley H. M., Artymiuk P. J., Rice D. W., Willett P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 1993; 229: 707–721
  • Gronbech-Jensen N., Doniach S. Long-time overdamped Langevin dynamics of molecular chains. J. Comp. Chem. 1994; 16: 997–1012
  • Gros P., van Gunsteren W. F. Crystatlo-graphic refinement and structure-factor time-averaging by molecular dynamics in the absence of a physical force field. Mol. Simul. 1993; 10: 377–395
  • Guamieri F., Still W. C. A rapidly convergent simulation method: mixed Monte Carlo/ stochastic dynamics. J. Comp. Chem. 1994; 15: 1302–1310
  • Gulukota K., Wolynes P. G. Statistical mechanics of kinetic proofreading in protein folding in vivo. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 9292–9296
  • Han K.-K., Martinage A. Possible relationship between coding recognition of amino acid sequence motif or residue(s) and post-translational chemical modification of proteins. Int. J. Biochem. 1992; 24: 1349–1363
  • Hancock J. F., Magee A. I., Childs J. E., Marshall C. J. All ras proteins are polyiso-prenylated but only some are palmitoylated. Cell 1989; 57: 1167–1177
  • Harrison R. W. Stiffness and energy conservation in molecular dynamics: an improved integrator. J. Comp. Chem. 1993; 14: 1112–1122
  • Hartl F. U. Secrets of a double-doughnut. Nature 1994; 371: 557–559
  • Harvey S. C. Treatment of electrostatic effects in macromolecular modeling. Proteins 1989; 5: 78–92
  • Havel T., Snow M. E. A new method for building protein conformations from sequence alignments with homologues of known structure. J. Mol. Biol. 1991; 217: 1–7
  • Hayward S., Collins J. F. Limits on α-helix prediction with neural network models. Proteins 1992; 14: 372–381
  • Head-Gordon T., Stillinger F. H., Arrecis J. A strategy for finding classes of minima on a hypersurface: implications for approaches to the protein folding problem. Proc. Natl. Acad. Sci. U. S. A. 1991; 88: 11076–11080
  • Head-Gordon T., Stilhger F. H. Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin. Biopolymers. 1993; 33: 293–303
  • Hellinga H. W., Richards F. M. Optimal sequence selection in proteins of known structure by simulated evolution. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 5803–5807
  • Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the structure of bacterior-hodopsin based on high-resolution electron cryo-microscopy. J. Mol. Biol. 1990; 213: 899–929
  • Hendlich M., Lackner P., Weitckus S., Floeckner H., Froschauer R., Gottsbacher K., Casari G., Sippl M. J. Identification of native protein folds among a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 1990; 216: 167–180
  • Henikoff S., Henikoff J. G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 10915–10919
  • Henikoff S., Henikoff J. G. Position-based sequence weights. J. Mol. Biol. 1994; 243: 574–578
  • Herczyk P., Hubbard R. E. A reduced representation of proteins for use in restraint satisfaction calculations. Proteins 1993; 17: 310–324
  • Hilbert M., Böhm G., Jaenicke R. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 1993; 17: 138–151
  • Hinds D. A., Levitt M. A lattice model for protein structure prediction at low resolution. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 2536–2540
  • Hinds D. A., Levitt M. Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 1994; 243: 668–682
  • Hirst J. D., Stemberg M. J. E. Prediction of structural and functional features of protein and nucleic acid sequences by neural networks. Biochemistry 1992; 31: 7211–7218
  • Holbrook S. R., Muskal S. M., Kim S.-H. Predicting surface exposure of amino acids from protein sequence. Prot. Eng. 1990; 3: 659–665
  • Holley L. H., Karplus M. Protein secondary structure prediction with a neural network. Proc. Natl. Acad. Sci. U. S. A. 1989; 86: 152–156
  • Holm L., Ouzounis C., Sander C., Tuparev G., Wend G. A database of protein structure families with common folding motifs. Prot. Sci. 1992; 1: 1691–1698
  • Holm L., Sander C. Fast and simple Monte Car 10 algorithm for side chain optimization in proteins: application to model building by homology. Proteins 1992a; 14: 213–223
  • Holm L., Sander C. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 1992b; 225: 93–105
  • Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993; 233: 123–138
  • Holm L., Sander C. The FSSP database of structurally aligned protein fold families. Nucl. Ac. Res. 1994a; 22: 3600–3609
  • Holm L., Sander C. Searching protein structure databases has come of age. Proteins 1994b; 19: 165–173
  • Holst M., Kozack R. E., Saied F., Subramaniam S. Treatment of electrostatics effects in proteins: multigrid-based Newton iterative method for solution of the full non-linear Poisson-Boltzmann equation. Proteins 1994a; 18: 231–245
  • Holst M., Kozack R. E., Saied F., Subramaniam S. Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. J. Biomol. Struct. Dyn. 1994b; 11: 1437–1445
  • Holst M., Saied F. Multigrid solution of the Poisson-Boltzmann equation. J. Comp. Chem. 1993; 14: 105–113
  • Hopp T. P. Retrospective: 12 years of Antigenic determinant predictions, and more. Peptide Res. 1993; 6: 183–190
  • Hopp T. P., Woods K. R. Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. U. S. A. 1981; 78: 3824–3828
  • Hubbard S. J., Eisenmenger F., Thomton J. M. Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Prot. Sci. 1994; 3: 757–768
  • Hucho F., Göme-Tschelnokow U., Strecker A. β-Structure in the membrane-spanning part of the nicotinic acetylcholine receptor (or how helical are transmembrane helices?). Trends Biochem. Sci. 1994; 19: 383–387
  • Jameson, Wolf H. The antigenic index: a novel algorithm for predicting antigenic determinants. Comput. Appl. Biosci. 1988; 4: 181–186
  • Janin J., Wodak S. J., Levitt M., Maigret M. Conformation of amino acid side-chains in proteins. J. Mol. Biol. 1978; 125: 357–386
  • Jenny T. F., Benner S. A. Evaluating predictions of secondary structure in proteins. Biophys. Biochem. Res. Comm. 1994; 200: 149–155
  • Johnson M. S., Overington J. P., Blundell T. L. Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 1993; 231: 735–752
  • Johnson M. S., Snnivasan N., Sowdhamini R., Blundell T. L. Knowledge-based protein modeling. Crit. Rev. Biochem. Mol. Biol. 1994; 29: 1–68
  • Johnson M. S., Overington J. P. A structural basis for sequence comparison. An evaluation of scoring methodologies. J. Mol. Biol. 1993; 233: 716–738
  • Johnson W. C., Jr. Protein secondary structure and circular dichroism: a practical guide. Proteins 1990; 7: 205–214
  • Jones D. T., Taylor W. R., Thomton J. M. A new approach to protein fold recognition. Nature 1992; 358: 86–89
  • Jones D. T. De novo protein design using pairwise potentials and a genetic algorithm. Prot. Sci. 1994; 3: 567–574
  • Jones T. A., Thirup S. Using known substructures in protein model building and crystallography. EMBO J. 1986; 5: 819–822
  • Juffer A. H., Botta E. F. F., van Keulen B. A. M., van der Ploeg A., Berendsen H. J. C. The electric potential of a macromolecule in a solvent: a fundamental approach. J. Comp. Phys. 1991; 97: 144–171
  • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 1976; A432: 922–923
  • Kabsch W., Sander C. How good are predictions of protein secondary structure. FEBS Lett. 1983a; 155: 179–182
  • Kabsch W., Sander C. Dictionary of protein secondary structures: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983b; 22: 2577–2637
  • Kabsch W., Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc. Natl. Acad. Sci. U. S. A. 1984; 81: 1075–1078
  • Kamimura M., Takahashi Y. phi-psi confor-mational pattern clustering of protein amino acid residues using the potential function method. Comput. Appl. Biosci. 1994; 10: 163–169
  • Kang H. A., Kurochkina N. A., Lee B. Estimation and use of protein backbone angle Drobabilities. J. Mol. Biol. 1993; 229: 448–460
  • Karlin S., Zuker M., Brocchieri L. Measuring residue associations in protein structures. Possible implications for protein folding. J. Mol. Biol. 1994; 239: 227–248
  • Karpen M. E., de Haseth P. L., Neet K. E. Comparing short protein substructures by a method based on backbone torsion angles. Proteins 1989; 6: 155–167
  • Karplus M., Ichiye T., Pettitt B. M. Con-figurational entropy of native proteins. Biophys. J. 1987; 52: 1083–1085
  • Karplus M., Schultz G. E. Prediction of chain flexibility in proteins. Naturwissenschaften 1985; 72: 212–213
  • Karshikov A. D., Engh R., Bode W., Atanasov B. P. Electrostatic interactions in proteins: calculations of the electrostatic term of free energy and the electrostatic potential field. Eur. Biophys. J. 1989; 17: 287–297
  • Kemp B. E., Pearson R. B. Protein kinase recognition sequence motifs. Trends Biochem. Sci. 1990; 15: 342–346
  • Kitao A., Hayward S., Go N. Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space. Biophys. Chem. 1994; 52: 107–114
  • Klein P. Prediction of protein structural class by discriminant analysis. Biochim. Biophys. Acta. 1986; 874: 205–215
  • Klein P., DeLisi C. Prediction of protein structural class from the amino acid sequence. Biopolymers 1986; 25: 1659–1672
  • Kneller D. G., Cohen F. E., Langridge R. Improvements in protein secondary structure prediction by enhanced neural networks. J. Mol. Biol. 1990; 214: 171–182
  • Kneller G. R., Geiger A. A method to calculate the g-coefficients of the molecular pair correlation function from molecular dynamics simulations. Mol. Simul. 1989; 3: 283–300
  • Kocher J.-P. A., Rooman M. J., Wodak S. J. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 1994; 235: 1598–1613
  • Koehl P., Delarue M. Polar and nonpolar atomic environments in the urotein core: implications for folding and binding. Proteins 1994a; 20: 264–278
  • Koehl P., Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 1994b; 239: 249–275
  • Kollman P. A., Dill K. A. J. Biomol. Struct. Dyn. 1991; 8: 1103–1107, Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn., 7.421 (1989))
  • Kono H., Doi J. Energy minimization method using automata network for sequence and side-chain confornation prediction. Proteins 1994; 19: 244–255
  • Kostrowicki J., Scheraga H. A. Application of the diffusion equation for global optimization to oligopeptides. J. Phys. Chem. 1992; 96: 7442–7449
  • Kiihlbrandt W., Wang D. N., Fujiyoshi Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature 1994; 367: 614–621
  • Kyte J., Doolittle R. F. A simple method for displaying the hydrophobic character of a protein. J. Mol. Biol. 1982; 157: 105–132
  • Lambert M. H., Scheraga H. A. Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability-directed search procedure. J. Comp. Chem. 1989; 10: 798–816
  • Lasters I., Desmet J. The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead end elimination theorem. Prot. Eng. 1993; 6: 717–722
  • Lathrop R. H. The protein threading problem with sequence amino acid interaction preferences is NP-complete. Prot. Eng. 1994; 7: 1059–1068
  • Lathrop R. H., Smith T. F. A branch-and-bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions. Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences. IEEE Computer Society Press, Los Alamos 1994; 365–374
  • Lau K. T., Dill K. A. Theory for protein mutability and biogenesis. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 638–642
  • Laughton C. A. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J. Mol. Biol. 1994a; 235: 1088–1097
  • Laughton C. A. A study of simulated annealing protocols for use with molecular dynamics in protein structure prediction. Prot. Eng. 1994b; 7: 235–241
  • Lavery R., Sklenar H., Zakrzewska K., Pullman B. The flexibility of nucleic acids. o. The calculation of internal energy and applications to mononucleotide repeat DNA. J. Biomol. Struct. Dyn. 1986; 3: 989–1014
  • Lee C., Subbiah S. Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 1991; 217: 373–388
  • Lee F. S., Chu Z. T., Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMM programs. J. Comp. Chem. 1993; 14: 161–185
  • Lee K. H., Xie D., Freire E., Amzel L. M. Estimation of changes in side chain configu-rational entropy in binding and folding: general methods and application to helix formation. Proteins 1994; 20: 68–84
  • Lemmon M. A., Engelmann D. M. Helix-helix interactions inside lipid bilayers. Curr. Opin. Struct. Biol. 1992; 2: 511–518
  • Leopold P. E., Montal M., Onuchic J. N. The protein folding funnels: a kinetic approach to the sequence-structure relationships. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 8721–8725
  • Lesk A. M., Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 1980; 136: 225–270
  • Lessel U., Schomburg D. Similarities between protein 3-D structures. Prot. Eng. 1994; 7: 1175–1187
  • Levin J. M., Pascarella S., Argos P., Gamier J. Quantification of secondary structure prediction improvement using multiple alignments. Prot. Eng. 1993; 6: 849–854
  • Levin J. M., Gamier J. Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim. Biophys. Acta. 1988; 955: 283–295
  • Levinthal C. Are there pathways for protein folding. J. Chem. Phys. 1968; 65: 44–45
  • Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 1976; 104: 59–107
  • Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 1992; 226: 507–533
  • Levitt M., Chothia C. Structural patterns in globular proteins. Nature 1976; 261: 552–558
  • Levitt M., Sharon R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. U. S. A. 1988; 85: 7557–7561
  • Li Z., Scheraga H. A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. U. S. A. 1987; 84: 6611–6615
  • Lim V. I. Algorithms for prediction of α-helical and β-structural regions in globular proteins. J. Mol. Biol. 1974; 88: 873–894
  • Lis H., Sharon N. Protein glycosylation. Structural and functional aspects. Eur. J. Biochem. 1993; 218: 1–27
  • Liwo A., Pincus M. R, Wawak R. J., Rackovsky S., Scheraga H. A. Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment. Prot. Sci. 1993; 2: 1697–1714
  • Luo Y., Jiang X., Lai L., Qu C., Xu X., Tang Y. Building protein backbones from Cα coordinates. Prot. Eng. 1992; 5: 147–150
  • Luo Y., Lai L., Xu X., Tang Y. Defining topological equivalences in protein structures by means of a dynamic programming algorithm. Prot. Eng. 1993; 6: 373–376
  • Luthardt G., Frömmel C. Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models. Prot. Eng. 1994; 7: 627–631
  • Lüthy R., McLachlan A. D., Eisenberg D. Secondary structure-based Protiles: use of structureconserving scoring tables in searching protein sequence databases for structural similarities. Proteins 1991; 10: 229–239
  • Lüthy R., Bowie J. U., Eisenberg D. Assessment of protein models with three-dimentional Protiles. Nature 1992; 356: 83–85
  • Lüthy R., Xenarios I., Bucher P. Improving the sensitivity of the sequence Protile method. Prot. Sci. 1994; 3: 139–146
  • Madej T., Mossing M. C. Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principle. J. Mol. Biol. 1993; 233: 480–487
  • Maiorov V. N., Crippen G. M. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 1992; 227: 876–888
  • Mandal C., Linthicum D. S. PROGEN: an automated modeling algorithm for the generation of complete protein structures from the α-carbon atomic coordinates. J. Comp.-Aid. Mol. Des. 1993; 7: 199–224
  • Mao B., Chou K.-C., Zhang C.-T. Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins. Prot. Eng. 1994; 7: 319–330
  • Mao B., Friedman A. R. Molecular dynamics simulation by atomic mass weighting. Biophys. J. 1990; 58: 803–805
  • Maple J. R., Hwang M.-H., Stockfish T. P., Bur U., Waldmann M., Ewig C. S., Hagler A. T. Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and the alkane molecules. J. Comp. Chem. 1994; 15: 162–180
  • Mark A. E., van Gunsteren W. F., Berendsen H. J. C. Calculation of relative free energy via indirect pathways. J. Chem. Phys. 1991; 94: 3808–3816
  • Matsuo Y., Kanehisa M. An approach to systematic detection of protein structural motifs. Comput. Appl. Biosci. 1993; 9: 153–159
  • Matsuo Y., Nishikawa K. Protein database search and structure prediction by 3D-1D compatibility method. Prot. Eng. 1994; 7: 1163
  • Matthew J. B. Electrostatic effects in proteins. Ann. Rev. Biophys. Biophys. Chem. 1985; 14: 387–417
  • May A. C. W., Johnson M. S. Protein structure comparisons using a combination of a genetic algorithm, dynamic programming and least-squares minimization. Prot. Eng. 1994; 7: 475–485
  • Mazur A. K., Dorofeev V. E., Abagyan R. A. Derivation and testing of explicit equations of motion for polymers described in internal coordinates. J. Comp. Phys. 1991; 92: 261–272
  • Marur A. K., Abagyan R. A. New methodology for computer-aided modeling of biomolecular structure and dynamics. I. Non-cyclic structures. J. Biomol. Struct. Dyn. 1989; 6(4)815–832
  • McGarrah D. B., Judson R. S. Analysis of the genetic algorithm method for molecular conformation determination. J. Comp. Chem. 1993; 14: 1385–1395
  • McGwzor M. J., Flores T. P., Sternberg M. J. E. Prediction of betaturns in proteins using neural networks. Prot. Eng. 1989; 2(7)521–526
  • McLachlan A. D. A mathematical procedure for superimposing atomic coordinates of proteins. Acta Cryst. 1972; A28: 656–657
  • McLachlan A. D. Rapid comparison of protein structures. Acta Cryst. 1982; 438: 871–873
  • Mehler E. L., Solmajer T. Electrostatic effects in proteins: comparison of dielectric and charge models. Prot. Eng. 1991; 4: 903–910
  • Metfessel B. A., Saurugger P. N., Connelly D. P., Rich S. S. Cross-validation of protein structural class prediction using statistical clustering and neural networks. Prot. Sci. 1993; 2: 1171–1182
  • Metropolis N., Rosenbluth A. W., Rosenbluth M. N., Teller A. H. Equation of state calculations for fast computing machines. J. Chem. Phys. 1953; 21: 1087–1092
  • Mezei M. Calculation of solvation free-energy differences for large solute change from computer simulations with quadrature-based nearly linear thermodynamic integration. Mol. Simul. 1993; 10: 225–239
  • Mezei M. A heuristic procedure for the detection of locally similar substructures of two equivalent structures. Prot. Eng. 1994; 7: 331–333
  • Mitchell E. M., Artymiuk P. J., Rice D. W., Willett P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 1989; 212: 151–166
  • Miyamoto S., Kollman P. A. SETTLE an analytical version of SHAKE and RATTLE algorithm for rigid water models. J. Comp. Chem. 1992; 13: 952–962
  • Miyazawa S., Jernigan R. L. Estimation of interresidue contact energies from protein crystal structures: quasichemical approximation. Macromolecules 1985; 18: 534–552
  • Monge A., Friesner R. A., Honig B. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 5027–5029
  • Moore C., Fasman G. D. The random coil conformation of proteins. Chemtracts -Biochem. Mol. Biol. 1993; 4: 67–74
  • Mottonen J., Strand A., Symerski J., Sweet R. M., Danley R. E., Geoghegen K. F., Gerard R. D., Goldsmith E. J. Structural basis of latency in plasrninogen activator inhibitor-1. Nature 1992; 355: 270–273
  • Moult J., James M. N. G. An algorithm for determining the conformation of polypeptide segemnts in proteins by systematic search. Proteins 1986; 1: 146–163
  • Muggleton S., King R. D., Sternberg M. J. E. Protein secondary structure prediction using logic-based machine learning. Prot. Eng. 1992; 5: 647–657
  • Muggleton S., King R. D., Sternberg M. J. E. Corrigenda: protein secondary structure prediction using logic-based machine learning. Prot. Eng. 1993; 6: 549
  • Murthy M. R. N. A fast method of comparing protein structures. FEBS Lett. 1984; 168: 97–102
  • Musacchio A., Gibson T. J., Rice P., Thompson J. D., Saraste M. The PHdomain: a common piece in the structural patchwork of signalling proteins. Trends Biochem. Sci. 1993; 18: 343–348
  • Muskal S. M., Kim S.-H. Predicting protein secondary structure content: a tandem neural network approach. J. Mol. Biol. 1992; 225: 713–727
  • Nagy P. L., Bitar J. E., Smith D. A. Comparison of the molecular mechanics + generalized Born/surface area and the ab initio + Monte Carlo simulation methods in estimating confonnational equilibria in aqueous solution. J. Comp. Chem. 1994; 15: 1228–1240
  • Nakashima H., Nahikawa K., Ooi T. The folding type of a protein is relevant to the amino acid composition. J. Biochem. 1986; 99: 153–162
  • Nayeem A., Vila J., Scheraga H. A. A comparative study of the simulated-annealing and Monte-Carlo-with-minimization approaches to the minimum-energy structures of polypep-tides: [Met]-enkephalin. J. Comp. Chem. 1991; 12: 594–605
  • Nemethy G., Pottle M. S., Scheraga H. A. Energy parameters in polypeptides. IX. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids. J. Phys. Chem. 1983; 87: 1883–1887
  • Nemethy G., Gibson K. D., Palmer K. A., Yoon C. N., Paterlini G., Zagari A., Rumsey S., Scheraga H. A. Energy parameters in polypeptides. X. Improved geometrical parameters and non-bonded interactions for use in the ECEPPD algorithm, with application to proline-containing peptides. J. Phys. Chem. 1992; 96: 6472–6484
  • Ngo T. J., Marks J. Computational complexity of a problem in molecular structure prediction. Prot. Eng. 1992; 5: 313–321
  • Nishikawa K., Kubota Y., Ooi T. Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types. J. Biochem. 1983a; 94: 997–1007
  • Nishikawa K., Kubota Y., Ooi T. Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution. J. Biochem. 1983b; 94: 981–995
  • Nishikawa K., Matsuo Y. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Prot. Eng. 1993; 6: 811–820
  • Nishikawa K., Ooi T. Correlation of the amino acid composition of a protein to its structural and biological characters. J. Biochem. 1982; 91: 1821–1824
  • Noguti T., Go N. Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins. Biopolymers 1985; 24: 527–546
  • Nonnan G. E., Podlipchuk V. Y., Valuev A. A. Equations of motion and energy conservation in molecular dynamics. Mol. Simul. 1994; 9: 417–424
  • Novomy J., Bruccoleri R. E., Karplus M. An analysis of incorrectly folded protein models. Implications for structure prediction. J. Mol. Biol. 1984; 177: 787–818
  • Novotny J., Rashin A. A., Bruccoleri R. E. Criteria that discriminate between native proteins and incorrectly folded models. Proteins 1988; 4: 13–30
  • Oberoi H., Allewell N. M. Multigrid solution of the nonlinear Poisson-Boltzmann equation and the calculation of titration curves. Biophys. J. 1993; 65: 48–55
  • Okamoto Y. Helix-forming tendencies of non-polar amino acids predicted by Monte Carlo simulated annealing. Proteins 1994; 19: 14–23
  • Okunbor D. I., Skeel R. D. Canonical numerical methods for molecular dynamics simulations. J. Comp. Chem. 1994; 15: 72–79
  • Olszewsky K. A., Piela L., Scheraga H. A. Mean field theory as a tool for inter-molecular conformational optimization. 1. Tests on terminally blocked alanine and Met-enkephalin. J. Phys. Chem. 1992; 96: 4672–4676
  • Ooi T., Oobatake M., Nemethy G., Scheraga H. A. Accessible surface areas as measure of the thermodynamic parameters of hydration of peptides. Proc. Natl. Acad. Sci. U. S. A. 1987; 84: 3086–3090
  • Orengo C. A., Brown N. P., Taylor W. R. Fast structure alignment for protein databank searching. Proteins 1992; 14: 139–167
  • Orengo C. A., Mores T. P., Taylor W. R., Thomton J. M. Identification and classification of protein fold families. Prot. Eng. 1993; 6: 485–500
  • Orengo C. A., Taylor W. R. A rapid method of protein structure alignment. J. Theor. Biol. 1990; 147: 517–551
  • Oroczo M., Luque F. J. Ab initio study of bond stretching: implications in force-field parametrization for molecular mechanics and dynamics. J. Comp. Chem. 1993; 14: 881–894
  • Ouzounis C., Sander C., Scharf M., Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact Protiles derived from three-dimensional structures. J. Mol. Biol. 1993; 232: 805–825
  • Overington J. P., Donelly D., Johnson M. S., Sali A., Blundell T. L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Prot. Sci. 1992; 1: 216–226
  • Pabo C. O. Designing proteins and peptides. Nature 1983; 301: 200
  • Pahe G. H., Scheraga H. A. Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. III. Probable and average conformations of enkephalin. Biopolymers 1987; 26: 1125–1162
  • Palmer K. A., Scheraga H. A. Standard geometry chains fitted to X-ray-derived structures: validation of the rigid geometry approximation. I. Chain closure through a l;imited search of “loop” conformations. J. Comp. Chem. 1991; 12: 505–526
  • Palmer K. A., Scheraga H. A. Standard geometry chains fitted to X-ray-derived structures: validation of the rigid-geometry approximation. II. Systematic searches for short loops in proteins: Application to bovine pancreatic ribonuclease A and human lysozyme. J. Comp. Chem. 1992; 13: 329–350
  • Pancoska P., Blazek M., Keiderling T. A. Relationships between secondary structure fractions for globular proteins. Neural network analysis of crystallographic data sets. Biochemistry 1992; 31: 10250–10257
  • Parker J. M. R., Guo D., Hodges R. S. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 1986; 25: 5425–5432
  • Pascarella S., Argos P. Analysis of insertions/deletions in proteins. J. Mol. Biol. 1992a; 224: 461–471
  • Pascarella S., Argos P. A data bank merging related protein structures and sequences. Prot. Eng. 1992b; 5: 121–137
  • Pastor R. W. Analyses of statistical errors in dynamics simulations. Proteins Structure, Dynamics and Design, V. Renugopalakrishnan, P. R. Carey, I. C. P. Smith, S. G. Huang, A. C. Storer. ESCOM, Leiden 1991; 229–233
  • Pastore A., Saudek V., Ramponi G., Williams R. J. P. Three-dimensional Structure of acylphosphatase. J. Mol. Biol. 1992; 224: 427–440
  • Patthy L. Exons—original building blocks of proteins. Bioessays 1991; 13: 187–192
  • Payne P. W. Reconstruction of protein conformations from estimated positions of the C, coordinates. Prot. Sci. 1993; 2: 315–324
  • Pearlman D. A. A comparison of alternative approaches to free energy calculations. J. Phys. Chem. 1994; 98: 1487–1493
  • Perczel A., Hollósi M., Tusnády G., Fasman G. D. Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Prot. Eng. 1991; 4: 669–679
  • Persson B., Flinta C., von Heijne G., Jömwall H. Structures of N-terminally acetylated proteins. Eur. J. Biochem. 1985; 152: 523–527
  • Persson B., Argos P. Prediction of trans-membrane regions in proteins utilising multiple sequence alignments. J. Mol. Biol. 1994; 237: 182–192
  • Pickett S. D., Saqi M. A. S., Sternberg M. J. E. Evaluation of the sequence template method for protein structure prediction. Discrimination of the (beta/alpha) 8-barrel fold. J. Mol. Biol. 1992; 228: 170–187
  • Pickett S. D., Sternberg M. I. E. Empirical scale of sidechain conformational entropy in protein folding. J. Mol. Biol. 1993; 231: 825–839
  • Picot D., Loll P. J., Garavito M. The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Nature 1994; 367: 243–249
  • Piela L., Kostrowicki J., Scheraga H. A. The multiple-minima problem in the conformational analysis of molecules. Determination of the potential energy surface by the diffusion equation. J. Phys. Chem. 1989; 93: 3339–3346
  • Pletnev V. Z., Popov E. M., Kadymova F. A. Approximated potential functions of non-bonded interactions of methyl groups. Theoret. Chim. Acta 1974; 35: 93–96
  • Ponder J. W., Richards F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 1987; 193: 775–791
  • Reissner R., Bork P. On α-helices terminated by glycine. I. Identification of common structural features. Biophys. Biochem. Res. Comm. 1991; 180: 660–665
  • Presnell S. R., Cohen B. I., Cohen F. E. A segment-based approach to protein secondary structure prediction. Biochemistry 1992; 31: 983–993
  • Purisima E. O., Scheraga H. A. Conversion from a virtual-bond chain to a complete polypeptide backbone. Biopolymers 1984; 23: 1207–1224
  • Purisima E. O., Scheraga H. A. An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin. J. Mol. Biol. 1987; 196: 697–709
  • Qian N., Sejnowski T. J. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 1988; 202: 865–884
  • Rao J. K., Argos P. A conformational preference parameter to predict helices in integral membrane proteins. Biochim. Biophys. Acta. 1986; 869: 197–214
  • Reczko M., Bohr H., Subramaniam S., Pamigighantam S., Hatzigeorgiou A. Fold-class prediction by neural networks. Protein structure by distance analysis, H. Bohr, S. Brunak. IOS Press, Amsterdam, Tokyo 1994; 277–286
  • Reczko M., Bohr H. The DEF data base of sequence based protein fold class predictions. Nucl. Acid. Res. 1994; 22: 3616–3619
  • Remington S. J., Matthews B. W. A systematic approach to the comparison of protein structures. J. Mol. Biol. 1980; 140: 77–99
  • Resh M. D. Myristylation and palmitylation of Src family members: the fats of the matter. Cell 1994; 76: 411–413
  • Rey A., Skolnick J. Efficient algorithm for reconstruction of a protein backbone from the α-carbon coordinates. J. Comp. Chem. 1992; 13: 443–456
  • Reynolds J. A., Gilbert D. B., Tanford C. Emprical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. U. S. A. 1974; 71: 2925–2927
  • Richards F. M., Kundrot C. E. Identification of structural motifs from protein coordinate data: secondary and first-level supersecondary structure. Proteins 1988; 3: 71–84
  • Richardson J. S. The anatomy and taxonomy of protein structure. Adv. Prot. Chem. 1981; 34: 168–339
  • Richardson J. S., Richardson D. C., Tweedy N. B., Gernet K. M., Quinn T. P., Hecht M. H., Ericson B. W., Yan Y., McClain R. D., Donlan M. E., Surles M. C. Looking at proteins: representations, folding, packing, and design. Biophys. J. 1992; 63: 1186–1209
  • Richmond T. J. Solvent accessible surface area and excluded volume in proteins. J. Mol. Biol. 1984; 178: 63–89
  • Ring C. S., Kneller D. G., Langridge R., Cohen F. E. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 1992; 224: 685–699
  • Ripoll D. R., Piela L., Vasquez M., Scheraga H. A. On the multiple minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte carlo methods to bovine pancreatic trypsin inhibitor. Proteins 1991; 10: 188–198
  • Robson B., Platt E. Relined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions with ore efficient calculations. J. Mol. Biol. 1986; 188: 259–281
  • Rohde K., Bork P. A fast, sensitive pattem-matching approach for protein sequences. Comput. Appl. Biosci. 1993; 9: 183–189
  • Roitberg A., Elber R. Modeling side chains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations. J. Chem. Phys. 1991; 95: 9277–9287
  • Rooman M. J., Kocher J.-P. A., Wodak S. J. Prediction of protein backbone conformations based on seven structure assignments. J. Mol. Biol. 1991; 221: 961–979
  • Rooman M. J., Kocher J.-P. A., Wodak S. J. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformations in the absence of tertiary interactions. Biochemistry 1992; 31: 10226–10238
  • Rooman M. J., Wodak S. J. Identification of predictive sequence motifs limited by protein structure database size. Nature 1988; 335: 45–49
  • Rose J., Eisenmenger F. A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm. J. Mol. Evol. 1994; 32: 340–354
  • Rossmann M. G., Argos P. Exploring structural homology of proteins. J. Mol. Biol. 1976; 105: 75–95
  • Rossmann M. G., Argos P. The taxonomy of protein structure. J. Mol. Biol. 1977; 109: 99–129
  • Rost B., Sander C., Schneider R. Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 1994; 235: 13–26
  • Rost B., Sander C. Secondary structure prediction of all-helical proteins in two states. Prot. Eng. 1993; 6: 831–836
  • Rost B., Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 1994a; 19: 55–72
  • Rost B., Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins 1994b; 20: 216–226
  • Rost B., Sander C. 1D secondary structure prediction through evolutionary Protiles. Protein structure by distance analysis, H. Bohr, S. Brunak. IOS Press, Amsterdam, Oxford, Tokyo 1994c; 257–216
  • Roterman L. K., Gibson K. D., Scheraga H. A. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9. J. Bio-mol. Struct. Dyn. 1989a; 7: 391–419
  • Roterman I. K., Lambert M. H., Gibson K. D., Scheraga H. A. A comparison of the CHARMM., AMBER and ECEPP potentials for peptides. II. phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. J. Bio-mol. Struct. Dyn. 1989b; 7: 421–453
  • Rudnicki W. R., Lesyng B., Harvey S. C. Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to pseudorotation dynamics of hose rings. Biopolymers 1994; 34: 383–392
  • Rufino S. D., Blundell T. L. Structure-based identification and clustering of protein farnilies and superfamilies. J. Comp.-Aid. Mol. Des. 1994; 8: 5–27
  • Russel R. B., Barton G. J. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts, secondary structure and accessibility. J. Mol. Biol. 1994; 244: 332–350
  • Russel R. B., Barton G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992; 14: 309–323
  • Russel R. B., Barton G. J. The limits of protein secondary structure prediction accuracy from multiple sequence alignments. J. Mol. Biol. 1993; 234: 951–957
  • Saitoh S., Nakai T., Nishikawa K. A geometrical constraint approach for reproducing the native backbone conformation of a protein. Proteins 1993; 15: 191–204
  • Sali A., Shakhnovich E., Karplus M. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 1994; 235: 1614–1636
  • Sali A., Blundell T. L. Definition of general topological equivalence in protein structures. A procedure involving comparison of prooperties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 1990; 212: 403–428
  • Sali A., Blundell T. L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 1993; 234: 779–815
  • Salzberg S., Cost S. Predicting protein secondary structure with a nearest-neighbor algorithm. J. Mol. Biol. 1992; 227: 371–374
  • Samorjai R. L. Novel approach for computing the global minimum of proteins. I. General concepts, methods and approximations. J. Phys. Chem. 1991; 95: 4141–4146
  • Sander C., Schneider R. Database of homol-ogy-derived protein structures and the structural meaning of sequence alignment. Proteins 1991; 9: 56–68
  • Schaefer M., Frömmel C. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solutions. J. Mol. Biol. 1990; 216: 1045–1066
  • Schiffer C. A., Caldwell J. W., Kollman P. A., Stroud R. M. Prediction of homologous pre tein structures based on conformational searches and energetics. Proteins 1990; 8: 30–43
  • Schiffer C. A., Caldwell J. W., Stroud R. M., Kollman P. A. Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as test case. Prot. Sci. 1992; 1: 396–400
  • Schiffer C. A., Caldwell J. W., Kollman P. A., Stroud R. M. Protein structure prediction with a combined solvation free energy-molecular mechanics force field. Mol. Simul. 1993; 10: 121–149
  • Schmitz U., Ulyanov N. B., Kumar A., James T. L. Molecular dynamics with weighted time-averaged restraints for a DNA octamer. J. Mol. Biol. 1993; 234: 373–389
  • Schrauber H., Eisenhaber F., Argos P. Rowers: to be or not to be? An analysis of amino acid sidechain conformations in globular proteins. J. Mol. Biol. 1993; 230: 592–612
  • Schreiber H., Steinhauser O. Taming cut-off induced artefacts in molecular dynamics studies of solvated polypeptides. J. Mol. Biol. 1992; 228: 909–923
  • Schroll W. K., Van Zandt L. L., Saxena V. K. Low-frequency parametrization of hydrogen bonding. J. Biomol. Struct. Dyn. 1991; 8: 1057–1067
  • Scully J. L., Hermans J. Multiple time steps: limits on the speedup of molecular dynamics simulations of aqueous systems. Mol. Simul. 1993; 11: 67–77
  • Shalloway D. Application of the renormalization group to deterministic global minimization of molecular conformation energy functions. J. Glob. Optim. 1992; 2: 281–311
  • Sheridan R. P., Dixon J. S., Venkataraghavan R., Kuntz I. D., Scott K. P. Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures. Biopolymers 1985; 24: 1995–2023
  • Shestopalov B. V. Prediction of protein secondary stucture by a doublet code. Mol. Biol. 1990; 24: 1117–1125
  • Shin J. K., Jhon M. S. High directional Monte Carlo procedure coupled with the temperature heating and annealing as a method to obtain the global energy minimum structure of polypeptides and proteins. Biopolymers 1991; 31: 177–185
  • Shake A., Rupley J. A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mot. Biol. 1973; 79: 351–371
  • Sibanda B. L., Thornton J. M. Conformation of beta-hairpins in protein structures: classifcation and diversity in homologous structures. Meth. Enzymol. 1991; 202: 59–82
  • Sibbald P., Argos P. Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol. 1990; 216: 813–818
  • Simon I., Glasser L., Scheraga H. A. Calculation of protein conformation as an assembly of stable overlapping segments: application to bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. U. S. A. 1991; 88: 3661–3665
  • Sipos L., von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 1993; 213: 1333–1340
  • Sippl M. J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 1990; 213: 859–883
  • Sippl M. J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comp.-Aid. Mol. Des. 1993a; 7: 473–501
  • Sippl M. J. Recognition of errors in threedimensional structures of proteins. Proteins 1993b; 17: 355–362
  • Sippl M. J., Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformation. Proteins 1992; 13: 258–271
  • Sklenar H., Etchebest C., Lavery R. Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 1989; 6: 46–60
  • Sklenar H., Eisenhaber F., Poncin M., Lavery R. Including solvent and counterion effects in the force field of macromolecular mechanics: the field integrated electrostatic approach (FIESTA). Theoretical Biochemistry & Molecular Biophysics, D. L. Beveridge, R. Lavery. Adenine Press, New York 1990; 317–335
  • Smith-Brown M. J., Kominos D., Levy R. M. Global folding of proteins from a limited number of distance constraints. Prot. Eng. 1993; 6: 605–614
  • Snow M. A novel parametrization scheme for energy equations and its use to calculate the structure of protein molecule. Proteins 1993; 15: 183–190
  • Solovyev V. V., Makarova K. S. A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization. Comput. Appl. Biosci. 1993; 9: 17–24
  • Sonnhammer E. L. L., Durbin R. A workbench for large-scale sequence homology analysis. Comput. Appl. Biosci. 1994; 10: 301–307
  • Sonnhammer E. L. L., Kahn D. The modular anangement of proteins as inferred from analysis of homology. Prot. Sci. 1994; 3: 482–492
  • Sreerama N., Woody R. W. Protein secondary structure from circular dichroism spec-troscopy. J. Mol. Biol. 1994; 242: 497–507
  • Starzyk R., Webster T., Schimmel P. Evidence for disposable sequences inserted into a nucleotide fold. Science 1987; 237: 1614–1618
  • Steinbach P. J., Brooks B. R. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 1994; 15: 667–683
  • Stemberg M. J. E., Chickos J. S. Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales. Prot. Eng. 1994; 7: 149–155
  • Stevens R. C., Gouaux J. E., Lipscomb W. N. Structural consequences of effector binding to the T state of aspartate carbamoyl-transferase: crystal structure of the unligated and ATP- and CTP-complexed enzymes at 2.6–Å resolution. Biochemistry 1990; 29: 7691–7701
  • Still W. C., Tempczyk A., Hawley R. C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem., Soc. 1990; 112: 6127–6129
  • Subbarao N., Haneef I. Defining to-pological equivalence in macromolecules. Prot. Eng. 1991; 4: 877–884
  • Summers N. L., Karplus M. Construction of side-chains in homology modeling. Application to the C-terminal lobe of rhizopuspepsin. J. Mol. Biol. 1989; 210: 785–811
  • Sun S. Reduced representation model pf protein structure prediction: statistical potential and genetic algorithm. Prot. Sci. 1993; 2: 762–785
  • Sutcliffe M. J., Hayes F. R. F., Blundell T. L. Knowledge-based modeling of homologous proteins. II: Rules for conformations of substituted side chains. Prot. Eng. 1987; 1: 385–392
  • Swindells M. B., Thornton J. M. A study of structural determinants in the interleukin-1 fold. Prot. Eng. 1993; 6: 711–715
  • Tanaka S., Scheraga H. A. Medium and long-range interaction parameters between amino acids for predicting three-dimensional structure of proteins. Macromolecules 1976; 9: 945–950
  • Tanford C., Kirkwood J. G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 1957; 79: 5333–5339
  • Taylor W. R. Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data. Prot. Eng. 1993; 6: 593–604
  • Taylor W. R., Orengo C. A holistic approach to protein structure alignment. Prot. Eng. 1989; 2: 505–519
  • Taylor W. R., Orengo C. A. Protein structure alignment. J. Mol. Biol. 1989; 208: 1–22
  • Thompson J. D., Higgins D. G., Gibson T. J. Improved sensitivity of pfle searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 1994; 10: 19–29
  • Toma K. Protein threedimensional structure generation with an empirical hydrophobic penalty function. J. Mol. Graph. 1994; 11: 222–232
  • Topham C. M., McLeod A., Eisenmenger F., Overington J. P., Johnson M. S., Blundell T. L. Fragment ranking in modeling of protein structure. Conformationally constrained environmental aminoacid substitution tables. J. Mol. Biol. 1993; 229: 194–220
  • Tramontano A., Chothia C., Lesk A. M. Structural determinants of the conformations of medium-sized loops in proteins. Proteins 1989; 6: 382–394
  • Tramontano A., Chothia C., Lesk A. M. Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the V, domains of the immunoglobulins. J. Mol. Biol. 1990; 215: 175–182
  • Tuffery P., Etchebest C., Hazout S., Lavery R. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 1991; 8: 1267–1289
  • Tuffery P., Etchebest C., Hazout S., Lavery R. A critical comparison of search algorithms applied to the optimization of protein side-chain conformations. J. Comp. Chem. 1993; 14: 790–798
  • Tunon I., Silla E., Pascual-Ahuir J. L. Molecular surface area and hydrophobic effect. Prot. Eng. 1992; 5: 715–716
  • Unger R., Moult J. Genetic algorithms for protein folding simulations. J. Mol. Biol. 1993; 231: 75–81
  • Unger R., Moult J. Finding the lowest free energy conformation is M NP-hard problem: proof and implications. Bull. Math. Biol. 1994; 55: 1183–1198
  • Vajda S., DeLisi C. Determining minimum energy confornations of polypeptides by dynamic programming. Biopolymers 1990; 29: 1755–1772
  • van Gelder C. W. G., Leusen F. J. J., Leunissen J. A. M., Noordik J. H. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data. Proteins 1994; 18: 174–185
  • van Gunsteren W. F., Berendsen H. J. C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 1977; 34: 1311–1327
  • van Gunsteren W. F., Berendsen H. J. C. Computer simulation of molecular dynamics: methodology, application and perspectives in chemistry. Angaw. Chem. Int. Ed. Engl. 1990; 29: 992–1023
  • van Heel M. A new family of powerful multivari-ate statistical sequence analysis (MSSA) techniques. J. Mol. Biol. 1992; 216: 877–887
  • van Schaik R. C., Berendsen H. J. C., Torda A. E., van Gunsteren W. F. A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 1993a; 234: 751–762
  • van Schaik R. C., van Gunsteren W. F., Berendsen H. J. C. Conformational search by potential energy annealing: algorithm and application to cyclosporin A. J. Comp.-Aid. Mol. Des. 1993b; 6: 97–112
  • Vandcrbilt D., Louie S. G. A Monte Carlo simulated annealing approach to optimization over continuous variables. J. Comp. Phys. 1984; 56: 259–271
  • Vasmatzis G., Brower R., De Lisi C. Predicting immunoglobulin-like hypervariable loops. Biopolymers 1994; 34: 1669–1680
  • Vasquez M., Scheraga H. A. Use of buildup and energy minimization procedures to compute low-energy structures of the backbone of enkephalin. Biopolymers 1985; 24: 1437–1447
  • Veenstra D. L., Ferguson D. M., Kollman P. A. How transferable are hydrogen parameters in molecular mechanics calculations. J. Comp. Chem. 1992; 13: 971–978
  • Venneri G. D., Hoover W. G. Simple exact test for well-known molecular dynamics algorithms. J. Comp. Phys. 1987; 73: 468–475
  • Vieth M., Kolinski A., Brooks C. L., III, Skolnick J. Prediction of the folding pathways and the structure of the GNC4 leu-cine zipper. J. Mol. Biol. 1994; 237: 361–367
  • Vila J., Williams R. L., Vasquez M., Scheraga H. A. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins 1991; 10: 199–218
  • von Freyberg B., Richmond T. J., Braun W. Surface area included in energy refinement of proteins. J. Mol. Biol. 1993; 233: 275–292
  • von Freyberg B., Braun W. Minimization of empirical energy functions including hydro-phobic surface area effects. J. Comp. Chem. 1993; 14: 510–521
  • von Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with trans-membrane topology. EMBO J. 1986; 5: 3021–3027
  • von Heijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 1992; 225: 487–494
  • Vorobyev Y. N., Grant J. A., Scheraga H. A. A combined iterative and boundary element approach for solution of the nonlinear Pois-son-Boltzmann equation. J. Am. Chem. Soc. 1992; 114: 3189–3196
  • Vriend G., Eijsink V. Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases. J. Comp.-Aid. Mol. Des. 1993; 7: 367–396
  • Vriend G., Sander C. Detection of common three-dimensional substructures in proteins. Proteins 1991; 11: 52–58
  • Vriend G., Sander C. Quality control of protein models: directional atomic contact analysis. J. Appl. Cryst. 1993; 26: 47–60
  • Wako H., Blundell T. L. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homo-logues proteins. I. Solvent accessibility classes. J. Mol. Biol. 1994a; 238: 682–692
  • Wako H., Blundell T. L. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures. J. Mol. Biol. 1994b; 238: 693–708
  • Wallqvist A. On the implementation of Friedman boundary conditions in liquid water simulations. Mol. Simul. 1993; 10: 13–17
  • Wallqvist A., Ullner M. A simplified amino acid potential for use in structure prediction of proteins. -Proteins 1994; 18: 267–280
  • Walther D. 1994, personal communication
  • Warshel A., Åqvist J. Electrostatic energy and macromolecular function. Ann. Rev. Biophys. Chem. 1991; 20: 267–298
  • Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A. An all atom force field for simulations of proteons and nucleic acids. J. Comp. Chem. 1986; 7: 230
  • Weiss M. S., Schulz G. E. Structure of poM refined at 1.8 Å resolution. J. Mol. Biol. 1992; 227: 493–509
  • Wendoloski J. J., Salemme F. R. PROBIT. a statistical approach to modeling proteins from partial coordinate data using substructure libraries. J. Mol. Graph. 1992; 10: 124–126
  • Wesson L., Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Prot. Sci. 1992; 1: 227–235
  • Wilmanns M., Eisenberg D. Threedimensional Protiles from residue-pair preferences: identification of sequences with beta/alfa-barrel fold. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 1379–1383
  • Wilson C., Gregoret L. M., Agard D. A. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol. 1993; 229: 9961–006
  • Wilson C., Cui W. Application of simulated annealing to peptides. Biopolymers 1990; 29: 149–157
  • Wilson C., Doniach S. A computer model to dynamically simulate protein folding: studies with crambin. Proteins 1989; 6: 193–209
  • Wodak S. J., Rooman M. J. Generating and testing protein folds. Curr. Opinion. Struct. Biol. 1993; 3: 247–259
  • Wootton J. C. Sequences with 'unusual' amino acid compositions. Cum. Opin. Struct. Biol. 1994; 4: 413–421
  • Ycas M. Computing tertiary structures of proteins. J. Prot. Chem. 1990; 9: 177–200
  • Yee D. P., Dill K. A. Families and the structural relatedness among globular proteins. Prot. Sci. 1993; 2: 884–899
  • Yi T.-M., Lander E. S. Protein structure prediction using nearest-neighbor methods. J. Mol. Biol. 1993; 232: 1117–1129
  • Yip V., Elber R. Calculations of a list of neighbors in molecular dynamics simulations. J. Comp. Chem. 1989; 10: 921–927
  • Zhang C.-T., Chou K.-C. Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. Biophys. J. 1992a; 63: 1523–1529
  • Zhang C.-T., Chou K.-C. An optimization approach to predicting protein structural class from amino acid composition. Prot. Sci. 1992b; 1: 401408
  • Zhang G., Schlick T. LIN: a new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques. J. Comp. Chem. 1993; 14: 1212–1233
  • Zhang K. Y. J., Eisenberg D. The threedimensional Protile method using residue preference as a continuous function of residue environment. Prot. Sci. 1994; 3: 687–695
  • Zhang T., Bertelsen E., Alber T. Entropic effects on disulfide bonds on protein stability. Nature Struct. Biol. 1994; 1: 434–438
  • Zhang X., Mesirov J. P., Waltz D. L. Hybrid system for protein secondary structure prediction. J. Mol. Biol. 1992; 225: 1049–1063
  • Zheng Q., Rosenfeld R., Vajda S., De Lisi C. Loop closure via bond scaling and relaxation. J. Comp. Chem. 1993a; 14: 556–565
  • Zheng Q., Rosenfeld R., Vajda S., De Lisi C. Determining protein loop conformation using scaling-relaxation techniques. Prot. Sci. 1993b; 2: 1242–1248
  • Zheng Q., Kyle D. J. Multiple copy sampling: rigid versus flexible protein. Proteins 1994; 19: 324–329
  • Zhong L., Johnson W. C., Jr. Environment affects amino acid preference for secondary stmcture. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 4462–4465
  • Zimmennann K. When awaiting ‘Bio’ Champollion: dynamic programming regularization of the protein secondary structure predictions. Prot. Eng. 1989; 7: 1197–1202
  • Zuker M., Somorjai R. L. The alignment of protein structures in three dimensions. Bull. Math. Biol. 1989; 51: 55–78

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.