Discrete analyses of protein dynamics

References

• Adzhubei, A. A. , & Sternberg, M. J. (1993). Left-handed polyproline II helices commonly occur in globular proteins. Journal of Molecular Biology , 229 (2), 472–493. doi:10.1006/jmbi.1993.1047
   PubMed Web of Science ®Google Scholar
• Aurora, R. , & Rose, G. D. (1998). Helix capping. Protein Science: A Publication of the Protein Society , 7 (1), 21–38. doi:10.1002/pro.5560070103
   PubMed Web of Science ®Google Scholar
• Barnoud, J. , Santuz, H. , Craveur, P. , Joseph, A. P. , Jallu, V. , de Brevern, A. G. , & Poulain, P. (2017). PBxplore: A tool to analyze local protein structure and deformability with protein blocks. PeerJ , 5 , e4013. doi:10.7717/peerj.4013
   PubMed Web of Science ®Google Scholar
• Benros, C. , de Brevern, A. G. , Etchebest, C. , & Hazout, S. (2005). Assessing a novel approach for predicting local 3D protein structures from sequence. Proteins: Structure, Function, and Bioinformatics , 62 (4), 865–880. doi:10.1002/prot.20815
   Web of Science ®Google Scholar
• Benros, C. , de Brevern, A. G. , & Hazout, S. (2009). Analyzing the sequence-structure relationship of a library of local structural prototypes. Journal of Theoretical Biology , 256 (2), 215–226. doi:10.1016/j.jtbi.2008.08.032
   PubMed Web of Science ®Google Scholar
• Benros, C. , Hazout, S. , & de Brevern, A. G. (2002). Extension of a local backbone description using a structural alphabet. “Hybrid Protein Model”: A new clustering approach for 3D local structures. Lyon, France: International Workshop on Bioinformatics ISMIS.
   Google Scholar
• Berendsen, H. J. C. , Postma, J. P. M. , van Gunsteren, W. F. , DiNola, A. , & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics , 81 (8), 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Berman, H. M. , Westbrook, J. , Feng, Z. , Gilliland, G. , Bhat, T. N. , Weissig, H. , … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research , 28 (1), 235–242. doi:10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Bornot, A. , & de Brevern, A. G. (2006). Protein beta-turn assignments. Bioinformation , 1 (5), 153–155. doi:10.6026/97320630001153
   PubMedGoogle Scholar
• Bornot, A. , Etchebest, C. , & de Brevern, A. G. (2009). A new prediction strategy for long local protein structures using an original description. Proteins: Structure, Function, and Bioinformatics , 76 (3), 570–587. doi:10.1002/prot.22370
   PubMed Web of Science ®Google Scholar
• Bornot, A. , Etchebest, C. , & de Brevern, A. G. (2011). Predicting protein flexibility through the prediction of local structures. Proteins: Structure, Function, and Bioinformatics , 79 (3), 839–852. doi:10.1002/prot.22922
   PubMed Web of Science ®Google Scholar
• Chandonia, J. M. , Hon, G. , Walker, N. S. , Lo Conte, L. , Koehl, P. , Levitt, M. , & Brenner, S. E. (2004). The ASTRAL Compendium in 2004. Nucleic Acids Research , 32 (Database issue), D189–D192. doi:10.1093/nar/gkh034
   PubMed Web of Science ®Google Scholar
• Chebrek, R. , Leonard, S. , de Brevern, A. G. , & Gelly, J. C. (2014). PolyprOnline: Polyproline helix II and secondary structure assignment database. Database (Database) , 2014 , bau102. doi:10.1093/database/bau102
   PubMedGoogle Scholar
• Chevrier, L. , de Brevern, A. , Hernandez, E. , Leprince, J. , Vaudry, H. , Guedj, A. M. , & de Roux, N. (2013). PRR repeats in the intracellular domain of KISS1R are important for its export to cell membrane. Molecular Endocrinology (Baltimore, Md.) , 27 (6), 1004–1014. doi:10.1210/me.2012-1386
   PubMedGoogle Scholar
• Colloc'h, N. , Etchebest, C. , Thoreau, E. , Henrissat, B. , & Mornon, J. P. (1993). Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment. Protein Engineering, Design and Selection , 6 , 377–382. doi:10.1093/protein/6.4.377
   Web of Science ®Google Scholar
• Craveur, P. , Gres, A. T. , Kirby, K. A. , Liu, D. , Hammond, J. A. , Deng, Y. , … Olson, A. J. (2019). Novel intersubunit interaction critical for HIV-1 core assembly defines a potentially targetable inhibitor binding pocket. mBio , 10 (2), e02858–18. doi:10.1128/mBio.02858-18
   PubMed Web of Science ®Google Scholar
• Craveur, P. , Joseph, A. P. , Esque, J. , Narwani, T. J. , Noel, F. , Shinada, N. , … de Brevern, A. G. (2015). Protein flexibility in the light of structural alphabets. Frontiers in Molecular Biosciences , 2 , 20.
   PubMed Web of Science ®Google Scholar
• Craveur, P. , Joseph, A. P. , Rebehmed, J. , & de Brevern, A. G. (2013). beta-Bulges: Extensive structural analyses of beta-sheets irregularities. Protein Science , 22 (10), 1366–1378. doi:10.1002/pro.2324
   PubMed Web of Science ®Google Scholar
• Craveur, P. , Rebehmed, J. , & de Brevern, A. G. (2014). PTM-SD: A database of structurally resolved and annotated posttranslational modifications in proteins. Database (Database) , 2014 (0), bau041. doi:10.1093/database/bau041
   PubMedGoogle Scholar
• Creamer, T. P. (1998). Left-handed polyproline II helix formation is (very) locally driven. Proteins , 33 (2), 218–226.
   PubMed Web of Science ®Google Scholar
• Darden, T. , Perera, L. , Li, L. , & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure , 7 (3), R55–R60. doi:10.1016/S0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• de Brevern, A. G. (2001). Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines. Biology (Analyses de Génomes et Modélisation Moléculaire). Paris, University Paris 7. PhD, 208.
   Google Scholar
• de Brevern, A. G. (2005). New assessment of a structural alphabet. In Silico Biology , 5 (3), 283–289.
   PubMedGoogle Scholar
• de Brevern, A. G. (2016). Extension of the classical classification of β-turns. Scientific Reports , 6 , 33191. doi:10.1038/srep33191
   PubMed Web of Science ®Google Scholar
• de Brevern, A. G. , Autin, L. , Colin, Y. , Bertrand, O. , & Etchebest, C. (2009). In silico studies on DARC. Infectious Disorders—Drug Targets , 9 (3), 289–303.
   PubMedGoogle Scholar
• de Brevern, A. G. , Camproux, A.-C. , Hazout, S. , Etchebest, C. , & Tuffery, P. (2001). Protein structural alphabets: Beyond the secondary structure description. In: S. Sangadai (Ed.), Recent research developments in protein engineering (Vol. 1, pp. 319–331). Trivandrum: Research Signpost.
   Google Scholar
• de Brevern, A. G. , Etchebest, C. , Benros, C. , & Hazout, S. (2007). Pinning strategy”: A novel approach for predicting the backbone structure in terms of protein blocks from sequence. Journal of Biosciences , 32 (1), 51–70. doi:10.1007/s12038-007-0006-3
   PubMed Web of Science ®Google Scholar
• de Brevern, A. G. , Etchebest, C. , & Hazout, S. (2000). Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins: Structure, Function, and Genetics , 41 (3), 271–287. doi:10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z
   PubMed Web of Science ®Google Scholar
• de Brevern, A. G. , & Hazout, S. (2003). Hybrid protein model' for optimally defining 3D protein structure fragments. Bioinformatics , 19 (3), 345–353. doi:10.1093/bioinformatics/btf859
   PubMed Web of Science ®Google Scholar
• de Brevern, A. G. , Valadie, H. , Hazout, S. , & Etchebest, C. (2009). Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship. Protein Science , 11 (12), 2871–2886. doi:10.1110/ps.0220502
   Web of Science ®Google Scholar
• de Brevern, A. G. , Wong, H. , Tournamille, C. , Colin, Y. , Le Van Kim, C. , & Etchebest, C. (2005). A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC). Biochimica et Biophysica Acta (Bba) – General Subjects , 1724 (3), 288–306. doi:10.1016/j.bbagen.2005.05.016
   PubMed Web of Science ®Google Scholar
• Dong, Q. W. , Wang, X. L. , & Lin, L. (2007). Methods for optimizing the structure alphabet sequences of proteins. Computers in Biology and Medicine , 37 (11), 1610–1616. doi:10.1016/j.compbiomed.2007.03.002
   PubMed Web of Science ®Google Scholar
• Donohue, J. (1953). Hydrogen bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences , 39 (6), 470–478. doi:10.1073/pnas.39.6.470
   PubMed Web of Science ®Google Scholar
• Dudev, M. , & Lim, C. (2007). Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites. BMC Bioinformatics , 8 (1), 106. doi:10.1186/1471-2105-8-106
   PubMed Web of Science ®Google Scholar
• Dupuis, F. , Sadoc, J. F. , & Mornon, J. P. (2004). Protein secondary structure assignment through Voronoi tessellation. Proteins: Structure, Function, and Bioinformatics , 55 (3), 519–528. doi:10.1002/prot.10566
   PubMed Web of Science ®Google Scholar
• Eisenberg, D. (2003). The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins. Proceedings of the National Academy of Sciences , 100 (20), 11207–11210. doi:10.1073/pnas.2034522100
   PubMed Web of Science ®Google Scholar
• Etchebest, C. , Benros, C. , Bornot, A. , Camproux, A. C. , & de Brevern, A. G. (2007). A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. European Biophysics Journal , 36 (8), 1059–1069. doi:10.1007/s00249-007-0188-5
   PubMed Web of Science ®Google Scholar
• Etchebest, C. , Benros, C. , Hazout, S. , & de Brevern, A. G. (2005). A structural alphabet for local protein structures: Improved prediction methods. Proteins: Structure, Function, and Bioinformatics , 59 (4), 810–827. doi:10.1002/prot.20458
   PubMed Web of Science ®Google Scholar
• Faure, G. , Bornot, A. , & de Brevern, A. G. (2008). Protein contacts, inter-residue interactions and side-chain modelling. Biochimie , 90 (4), 626–639. doi:10.1016/j.biochi.2007.11.007
   PubMed Web of Science ®Google Scholar
• Fernandez-Fuentes, N. , Querol, E. , Aviles, F. X. , Sternberg, M. J. , & Oliva, B. (2005). Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops. Proteins: Structure, Function, and Bioinformatics , 60 (4), 746–757. doi:10.1002/prot.20516
   PubMed Web of Science ®Google Scholar
• Fourrier, L. , Benros, C. , & de Brevern, A. G. (2004). Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics , 5 (1), 58.
   PubMed Web of Science ®Google Scholar
• Fox, N. K. , Brenner, S. E. , & Chandonia, J. M. (2014). SCOPe: Structural *Classification of Proteins–extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research , 42 (D1), D304–D309. doi:10.1093/nar/gkt1240
   PubMed Web of Science ®Google Scholar
• Frishman, D. , & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins: Structure, Function, and Genetics , 23 (4), 566–579. doi:10.1002/prot.340230412
   PubMed Web of Science ®Google Scholar
• Ghouzam, Y. , Postic, G. , de Brevern, A. G. , & Gelly, J. C. (2015). Improving protein fold recognition with hybrid profiles combining sequence and structure evolution. Bioinformatics , 31 , 3782–3789.
   PubMed Web of Science ®Google Scholar
• Ghouzam, Y. , Postic, G. , Guerin, P. E. , de Brevern, A. G. , & Gelly, J. C. (2016). ORION: A web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. Scientific Reports , 6 (1), 28268. doi:10.1038/srep28268
   PubMed Web of Science ®Google Scholar
• Goguet, M. , Narwani, T. J. , Petermann, R. , Jallu, V. , & de Brevern, A. G. (2017). In silico analysis of Glanzmann variants of Calf-1 domain of alphaIIbbeta3 integrin revealed dynamic allosteric effect. Scientific Reports , 7 (1), 8001. doi:10.1038/s41598-017-08408-w
   PubMed Web of Science ®Google Scholar
• Hartigan, J. A. , & Wong, M. A. (1979). A K-means clustering algorithm. Applied Statistics , 28 , 100–108. doi:10.2307/2346830
   Google Scholar
• Hensen, U. , Meyer, T. , Haas, J. , Rex, R. , Vriend, G. , & Grubmuller, H. (2012). Exploring protein dynamics space: The dynasome as the missing link between protein structure and function. PLoS One , 7 (5), e33931. doi:10.1371/journal.pone.0033931
   PubMed Web of Science ®Google Scholar
• Hermoso, A. , Espadaler, J. , Enrique Querol, E. , Aviles, F. X. , Sternberg, M. J. , Oliva, B. , & Fernandez-Fuentes, N. (2009). Including functional annotations and extending the collection of structural classifications of protein loops (ArchDB). Bioinformatics and Biology Insights , 1 , 77–90. doi:10.1177/117793220700100004
   PubMedGoogle Scholar
• Hess, B. , Bekker, H. , Berendsen, H. J. C. , & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 (12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
   Web of Science ®Google Scholar
• Hosseini, S. R. , Sadeghi, M. , Pezeshk, H. , Eslahchi, C. , & Habibi, M. (2008). PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms. Computational Biology and Chemistry , 32 (6), 406–411. doi:10.1016/j.compbiolchem.2008.07.027
   PubMed Web of Science ®Google Scholar
• Hutchinson, E. G. , & Thornton, J. M. (2008). PROMOTIF—A program to identify and analyze structural motifs in proteins. Protein Science , 5 (2), 212–220. doi:10.1002/pro.5560050204
   Google Scholar
• Jallu, V. , Poulain, P. , Fuchs, P. F. , Kaplan, C. , & de Brevern, A. G. (2012). Modeling and molecular dynamics of HPA-1a and -1b polymorphisms: Effects on the structure of the β3 subunit of the αIIbβ3 integrin. PLoS One , 7 (11), e47304. doi:10.1371/journal.pone.0047304
   PubMed Web of Science ®Google Scholar
• Jallu, V. , Poulain, P. , Fuchs, P. F. , Kaplan, C. , & de Brevern, A. G. (2014). Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit beta3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants. Biochimie , 105 , 84–90. doi:10.1016/j.biochi.2014.06.017
   PubMed Web of Science ®Google Scholar
• Jonsson, A. L. , Scott, K. A. , & Daggett, V. (2009). Dynameomics: A consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Biophysical Journal , 97 (11), 2958–2966.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L. , & Madura, J. D. (1983). Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water. Journal of the American Chemical Society , 105 (6), 1407–1413.
   Web of Science ®Google Scholar
• Joseph, A. P. , Agarwal, G. , Mahajan, S. , Gelly, J. C. , Swapna, L. S. , Offmann, B. , … De Brevern, A. G. (2010). A short survey on protein blocks. Biophysical Reviews , 2 (3), 137–147. doi:10.1007/s12551-010-0036-1
   PubMedGoogle Scholar
• Joseph, A. P. , Bornot, A. , & de Brevern, A. G. (2010). Local structure alphabets. Protein structure prediction H. Rangwala and G. Karypis , Hoboken, NJ: Wiley.
   Google Scholar
• Kabsch, W. , & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers , 22 (12), 2577–2637. doi:10.1002/bip.360221211
   PubMed Web of Science ®Google Scholar
• Karchin, R. , Cline, M. , Mandel-Gutfreund, Y. , & Karplus, K. (2003). Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry. Proteins: Structure, Function, and Bioinformatics , 51 (4), 504–514. doi:10.1002/prot.10369
   PubMed Web of Science ®Google Scholar
• Labesse, G. , Colloc'h, N. , Pothier, J. , & Mornon, J. P. (1997). P-SEA: A new efficient assignment of secondary structure from C alpha trace of proteins. Bioinformatics , 13 , 291–295. doi:10.1093/bioinformatics/13.3.291
   Google Scholar
• Ladislav, M. , Cerny, J. , Krusek, J. , Horak, M. , Balik, A. , & Vyklicky, L. (2018). The LILI *Motif of M3-S2 linkers is a component of the NMDA receptor channel gate. Frontiers in Molecular Neuroscience , 11 , 113. doi:10.3389/fnmol.2018.00113
   PubMed Web of Science ®Google Scholar
• Leonard, S. , Joseph, A. P. , Srinivasan, N. , Gelly, J. C. , & de Brevern, A. G. (2014). mulPBA: An efficient multiple protein structure alignment method based on a structural alphabet. Journal of Biomolecular Structure and Dynamics , 32 , 661–668. doi:10.1080/07391102.2013.787026
   PubMed Web of Science ®Google Scholar
• Levitt, M. , & Greer, J. (1977). Automatic identification of secondary structure in globular proteins. Journal of Molecular Biology , 114 (2), 181–239. doi:10.1016/0022-2836(77)90207-8
   PubMed Web of Science ®Google Scholar
• Li, Q. , Zhou, C. , & Liu, H. (2009). Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities. Proteins: Structure, Function, and Bioinformatics , 74 (4), 820–836. doi:10.1002/prot.22191
   PubMed Web of Science ®Google Scholar
• Mahajan, S. , de Brevern, A. G. , Sanejouand, Y. H. , Srinivasan, N. , & Offmann, B. (2015). Use of a structural alphabet to find compatible folds for amino acid sequences. Protein Science , 24 (1), 145–153. doi:10.1002/pro.2581
   PubMed Web of Science ®Google Scholar
• Mansiaux, Y. , Joseph, A. P. , Gelly, J. C. , & de Brevern, A. G. (2011). Assignment of PolyProline II conformation and analysis of sequence–structure relationship. PLoS One , 6 (3), e18401. doi:10.1371/journal.pone.0018401
   PubMed Web of Science ®Google Scholar
• Martin, J. , Letellier, G. , Marin, A. , Taly, J. F. , de Brevern, A. G. , & Gibrat, J. F. (2005). Protein secondary structure assignment revisited: A detailed analysis of different assignment methods. BMC Structural Biology , 5 (1), 17. doi:10.1186/1472-6807-5-17
   PubMed Web of Science ®Google Scholar
• Narwani, T. J. , Craveur, P. , Shinada, N. K. , Santuz, H. , Rebehmed, J. , Etchebest, C. , & de Brevern, A. G. (2018). Dynamics and deformability of α-, 310- and π-helices. Archives of Biological Sciences , 70 (1), 21–31. doi:10.2298/ABS170215022N
   Web of Science ®Google Scholar
• Narwani, T. J. , Santuz, H. , Shinada, N. , Vattekatte, A. M. , Ghouzam, Y. , Srinivasan, N. , … de Brevern, A. G. (2017). Recent advances on PolyProline II. Amino Acids , 49 (4), 705–713. doi:10.1007/s00726-017-2385-6
   PubMed Web of Science ®Google Scholar
• Offmann, B. , Tyagi, M. , & de Brevern, A. G. (2007). Local protein structures. Current Bioinformatics , 3 , 165–202. doi:10.2174/157489307781662105
   Web of Science ®Google Scholar
• Pal, L. , & Basu, G. (1999). Novel protein structural motifs containing two-turn and longer 3(10)-helices. Protein Engineering, Design and Selection , 12 (10), 811–814. doi:10.1093/protein/12.10.811
   Web of Science ®Google Scholar
• Pal, L. , Basu, G. , & Chakrabarti, P. (2002). Variants of 3(10)-helices in proteins. Proteins , 48 (3), 571–579. doi:10.1002/prot.10184
   PubMed Web of Science ®Google Scholar
• Pal, L. , Chakrabarti, P. , & Basu, G. (2003). Sequence and structure patterns in proteins from an analysis of the shortest helices: Implications for helix nucleation. Journal of Molecular Biology , 326 (1), 273–291. doi:10.1016/S0022-2836(02)01338-4
   PubMed Web of Science ®Google Scholar
• Pancsa, R. , Raimondi, D. , Cilia, E. , & Vranken, W. F. (2016). Early folding events, local interactions, and conservation of protein backbone rigidity. Biophysical Journal. 110 (3), 572–583. doi:10.1016/j.bpj.2015.12.028
   PubMed Web of Science ®Google Scholar
• Pandurangan, S. , Meganathan, I. , Ragavan, S. , Ramudu, K. N. , Shanmugam, E. , Shanmugam, G. , & Niraikulam, A. (2019). Engineering of a skin-fiber-opening enzyme for sulfide-free leather beam house operation through xenobiology. Green Chemistry , 21 (8), 2070–2081. doi:10.1039/C8GC03479F
   Web of Science ®Google Scholar
• Park, S. Y. , Yoo, M. J. , Shin, J. , & Cho, K. H. (2011). SABA (secondary structure assignment program based on only alpha carbons): A novel pseudo center geometrical criterion for accurate assignment of protein secondary structures. BMB Reports , 44 (2), 118–122. doi:10.5483/BMBRep.2011.44.2.118
   PubMed Web of Science ®Google Scholar
• Parrinello, M. , & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics , 52 (12), 7182–7190. doi:10.1063/1.328693
   Web of Science ®Google Scholar
• Pauling, L. , & Corey, R. B. (1951). The pleated sheet, a new layer configuration of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America , 37 (5), 251–256. doi:10.1073/pnas.37.5.251
   PubMed Web of Science ®Google Scholar
• Pauling, L. , Corey, R. B. , & Branson, H. R. (1951). The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences , 37 (4), 205–211. doi:10.1073/pnas.37.4.205
   PubMed Web of Science ®Google Scholar
• Pronk, S. , Pall, S. , Schulz, R. , Larsson, P. , Bjelkmar, P. , Apostolov, R. , … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics , 29 (7), 845–854. doi:10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Rangwala, H. , Kauffman, C. , & Karypis, G. (2009). svmPRAT: SVM-based protein residue annotation toolkit. BMC Bioinformatics , 10 (1), 439. doi:10.1186/1471-2105-10-439
   PubMed Web of Science ®Google Scholar
• Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advances in Protein Chemistry , 34 , 167–339.
   PubMedGoogle Scholar
• Richardson, J. S. , & Richardson, D. C. (1988). Amino acid preferences for specific locations at the ends of alpha helices. Science , 240 (4859), 1648–1652. doi:10.1126/science.3381086
   PubMed Web of Science ®Google Scholar
• Rooman, M. J. , Rodriguez, J. , & Wodak, S. J. (1990). Relations between protein sequence and structure and their significance. Journal of Molecular Biology , 213 (2), 337–350. doi:10.1016/S0022-2836(05)80195-0
   PubMed Web of Science ®Google Scholar
• Schneider, B. , Černý, J. , Svozil, D. , Čech, P. , Gelly, J.-C. , & de Brevern, A. G. (2014). Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Research , 42 (5), 3381–3394. doi:10.1093/nar/gkt1273
   PubMed Web of Science ®Google Scholar
• Schneider, B. , Gelly, J. C. , de Brevern, A. G. , & Černý, J. (2014). Local dynamics of proteins and DNA evaluated from crystallographic B factors. Acta Crystallographica. Section D, Biological Crystallography , 70 (Pt 9), 2413–2419. doi:10.1107/S1399004714014631
   PubMedGoogle Scholar
• Sklenar, H. , Etchebest, C. , & Lavery, R. (1989). Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins: Structure, Function, and Genetics , 6 (1), 46–60. doi:10.1002/prot.340060105
   PubMed Web of Science ®Google Scholar
• Thomas, A. , Deshayes, S. , Decaffmeyer, M. , Van Eyck, M. H. , Charloteaux, B. , & Brasseur, R. (2006). Prediction of peptide structure: How far are we? Proteins , 65 (4), 889–897. doi:10.1002/prot.21151
   PubMed Web of Science ®Google Scholar
• Touw, W. G. , Baakman, C. , Black, J. , Te Beek, T. A. , Krieger, E. , Joosten, R. P. , & Vriend, G. (2015). A series of PDB-related databanks for everyday needs. Nucleic Acids Research , 43 (D1), D364–D368. doi:10.1093/nar/gku1028
   PubMed Web of Science ®Google Scholar
• Tyagi, M. , Bornot, A. , Offmann, B. , & de Brevern, A. G. (2009a). Analysis of loop boundaries using different local structure assignment methods. Protein Science , 18 (9), 1869–1881. doi:10.1002/pro.198
   PubMed Web of Science ®Google Scholar
• Tyagi, M. , Bornot, A. , Offmann, B. , & de Brevern, A. G. (2009b). Protein short loop prediction in terms of a structural alphabet. Computational Biology and Chemistry , 33 (4), 329–333. doi:10.1016/j.compbiolchem.2009.06.002
   PubMed Web of Science ®Google Scholar
• Tyagi, M. , de Brevern, A. G. , Srinivasan, N. , & Offmann, B. (2008). Protein structure mining using a structural alphabet. Proteins: Structure, Function, and Bioinformatics , 71 (2), 920–937. doi:10.1002/prot.21776
   PubMed Web of Science ®Google Scholar
• Tyagi, M. , Gowri, V. S. , Srinivasan, N. , de Brevern, A. G. , & Offmann, B. (2006). A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications. Proteins: Structure, Function, and Bioinformatics , 65 (1), 32–39. doi:10.1002/prot.21087
   PubMed Web of Science ®Google Scholar
• Tyagi, M. , Sharma, P. , Swamy, C. S. , Cadet, F. , Srinivasan, N. , de Brevern, A. G. , & Offmann, B. (2006). Protein block expert (PBE): A web-based protein structure analysis server using a structural alphabet. Nucleic Acids Research , 34 (Web Server), W119–W123. doi:10.1093/nar/gkl199
   PubMed Web of Science ®Google Scholar
• Unger, R. , Harel, D. , Wherland, S. , & Sussman, J. L. (1989). A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins: Structure, Function, and Genetics , 5 (4), 355–373. doi:10.1002/prot.340050410
   PubMed Web of Science ®Google Scholar
• van der Kamp, M. W. , Schaeffer, R. D. , Jonsson, A. L. , Scouras, A. D. , Simms, A. M. , Toofanny, R. D. , … Daggett, V. (2010). Dynameomics: A comprehensive database of protein dynamics. Structure , 18 (4), 423–435. doi:10.1016/j.str.2010.01.012
   PubMed Web of Science ®Google Scholar
• van Gunsteren, W. F. , Billeter, S. R. , Eising, A. A. , Hünenberger, P. H. , Krüger, P. , Mark, A. E. , … Tironi, I. G. (1996). Biomolecular Simulation: The GROMOS96 Manual and User Guide. 1042.
   Google Scholar
• Venkatachalam, C. M. (1968). Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers , 6 (10), 1425–1436. doi:10.1002/bip.1968.360061006
   PubMed Web of Science ®Google Scholar
• Vetrivel, I. , Mahajan, S. , Tyagi, M. , Hoffmann, L. , Sanejouand, Y. H. , Srinivasan, N. , … Offmann, B. (2017). Knowledge-based prediction of protein backbone conformation using a structural alphabet. PLoS One , 12 (11), e0186215. doi:10.1371/journal.pone.0186215
   PubMed Web of Science ®Google Scholar
• Zimmermann, O. , & Hansmann, U. H. (2008). LOCUSTRA: Accurate prediction of local protein structure using a two-layer support vector machine approach. The Journal of Chemical Information and Modeling , 48 (9), 1903–1908.
   PubMed Web of Science ®Google Scholar
• Zuo, Y. C. , & Li, Q. Z. (2009a). Using K-minimum increment of diversity to predict secretory proteins of malaria parasite based on groupings of amino acids. Amino Acids , 38(3), 859–867. doi:10.1007/s00726-009-0292-1
   PubMed Web of Science ®Google Scholar
• Zuo, Y. C. , & Li, Q. Z. (2009b). Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet. Peptides , 30 (10), 1788–1793. doi:10.1016/j.peptides.2009.06.032
   PubMed Web of Science ®Google Scholar