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Original Articles

Preliminary Analysis of Water Molecule Distributions in Proteins

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Pages 167-182 | Received 01 Jan 1988, Accepted 01 May 1988, Published online: 23 Sep 2006

References

  • Goodfellow , J. M. , Finney , J. L. and Barnes , P. 1982 . Monte Carlo Computer Simulation of Water-Amino Acid Interactions” . Proc. Roy. Soc , B214 : 213
  • Goodfellow , J. M. 1987 . “Computer Simulation of Hydration Networks around Amino Acids” . Int. J. Biol, Macro. , 9 : 273
  • Hagler , A. T. , Moult , J. and Osguthorpe , D. J. 1980 . “Monte Carlo Simulation of the Solvent Structure in Crystals of a Hydrated Cyclic Peptide” . Biopolymers , 19 : 395
  • Rossky , P. and Karplus , M. 1979 . “Solvation. A Molecular Dynamics Study of a Dipeptide in Water” . J. Am. Chem. Soc , 101 : 1913
  • Elliott , R. J. and Goodfellow , J. M. 1987 . “Monte Carlo Simulation of Nucleotide Crystal Hydrates and their counter-ions” . J. Theor. Biol , 127 : 403
  • Beveridge , D. L. , Maye , P. V. , Jayaram , B. , Ravishanker , G. and Mezei . 1984 . “Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Simulation Studies” . J. Biomol. Struc. & Dyn. , 2 : 261
  • Hagler , A. T. and Moult , J. 1979 . “Computer Simulation of the Solvent Structure around Biological Macro-molecules” . Nature , 272 : 222
  • van Gunsteren , W. F. , Berendsen , H. J. C. , Hermans , J. , Hol , W. G. J. and Postma , J. P. M. 1983 . “Computer Simulation of the Dynamics of Hydrated Protein Crystals and its Comparison with x-ray data” . Proc. Natl. Acad. Sci , 80 : 4315
  • Momany , F. A. , McGuire , R. F. , Burgess , A. W. and Scheraga , H. A. 1975 . “Energy Parameters in Polypeptides VII” . J. phys. Chem , 79 : 2361
  • Lifson , S. , Hagler , A. T. and Dauber , P. 1979 . “Consistent Force Field Studies of Intermolecular Forces in Hydrogen Bonded Crystals” . J. Am. Chem. Soc. , 53 : 4544
  • Weiner , S. J. , Kollman , P. A. , Nguyen , D. T. and Case , D. A. 1986 . “An All Atom Force Field for Simulations of Proteins and Nucleic Acids” . J. Comp. Chem. , 7 : 230
  • Jorgensen , W. L. and Swenson , C. J. 1985 . “Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides” . J. Am. Chem. Soc. , 107 : 1489
  • Finney , J. L. , Quinn , J. E. and Baum , J. O. 1986 . “The Water Dimer Potential Surface” . Water Sci. Rev. , 1 : 33
  • Finney , J. L. , Howell , J. M. , Goodfellow , P. L. and Vovelle , F. 1985 . “Computer Simulation of Aqueous Biomolecular Systems” . J. Biomol. Struct. & Dyn. , 3 : 599
  • Savage , H. 1986 . “Water Structure in Vitamin B12 Coenzyme Crystals” . Biophys. J. , 50 : 947
  • Edsall , J. T. and McKenzie , H. A. 1978 . “Water and Proteins I” . Adv. Biophys. , 10 : 137
  • Edsall , J. T. and McKenzie , H. A. 1983 . “Water and Proteins II” . Adv. Biophys , 16 : 53
  • Finney , J. L. 1979 . “Organization and Function of Water in Protein Crystals” . In ‘Water. A Comprehensive Treatise’ , Edited by: Franks , F. vol 6 , 47 – 122 . Plenum .
  • Baker , E. N. and Hubbard , R. E. 1984 . “Hydrogen Bonding in Globular Proteins” . Prog. Biophys. Mol. Biol. , 44 : 97
  • Saenger , W. 1987 . “Structure and Dynamics of Water Surrounding Biomolecules” . Ann. Rev. Biophy , 93 : 114
  • Bernstein , F. C. , Koetzle , T. F. , Williams , G. J. B. , Meyer , E. F. , Brice , M. D. , Rodgers , J. R. , Kennard , O. , Shimanouchi , T. and Tasumi , M. 1977 . “The Protein Data Bank: A computer-based Archival File for Macromolecular Structure” . J. Mol. Biol , 112 : 535
  • Jones , T. A. 1978 . “A Graphics Model Building and Refinement System for Macromolecules” . J. Appl. Cryst , 11 : 268
  • Powell , M. J. D. 1964 . “An efficient method for finding the minimum of a function of several variables without calculating derivatives” . Computer Journal , 7 : 155
  • Jorgensen , W. L. , Chandrashekhar , J. , Madura , J. D. , Impey , R. and Klein , M. L. 1983 . “Comparison of Simple Functions for Simulating Liquid Water” . J. Chem. Phys. , 79 : 926
  • McGregor , M. J. , Islam , S. A. and Sternberg , M. J. E. 1987 . “Analysis of the Relationship between Side-Chain Conformation and Secondary Structure in Globular Proteins” . J. Mol. Biol. , 198 : 295
  • Kabsch , W. and Sander , C. 1983 . “Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features” . Biopolymers , 22 : 2577
  • Goodford , P. J. 1985 . “A Computational Procedure for Determining Energetically Favourable Binding Sites on Biologically Important Macromolecules” . J. Med. Chem. , 28 : 849

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