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References
Acharya, K.R., Ren J.S., Stuart, D.I., Phillips, D.C. and Fenna, R.E. (1991). Crystal structure of human alpha-lactalbumin at 1.7 A resolution. J Mol Biol 221(2): 571–81.
Alexandrov, N.N., Takahashi, K., et al. (1992). Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. J Mol Biol 225(1): 5–9.
Aloyand, P. and Russell, R.B. (2003). InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19(1): 161–162.
Aloy, P., Stark, A., et al. (2003). Predictions without templates: new folds, secondary structure, and contacts in CASP5. proteins 53: 436–456.
Bateman, A., Coin, L., et al. (2004). The Pfam protein families database. Nucleic Acids Res 32Database issue: D138–41.
Berman, H.M., Westbrook, J., et al. (2000). The Protein Data Bank. Nucleic Acids Res 28(1): 235–42.
Bernstein, F.C., Koetzle, T.F., et al. (1977). The Protein Data Bank: a computerbased archival file for macromolecular structures. J Mol Biol 112(3): 535–42.
Bohacek, R.S. and C. McMartin (1994). Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of de novo design method incorporating combinatorial grow. J Am Chem Soc 116: 5560–71.
Bourne, P.E. (1999). Bioinformatics 15: 715–6.
Bourne, P.E., Addess, K.J., et al. (2004). The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res 32Database issue: D223–5.
Bourne, P.E., Berman, H.M., et al. (1997). The macromolecular Crystallographic Information File (mmCIF).
Bourne, P.E. and Weissig, H. Eds. (2003). Structural Bioinformatics. Hoboken, NJ, Wiley-Liss, Inc.
Burley, S.K., Almo, S.C., et al. (1999). Structural genomics: beyond the human genome project. Nat Genet 23: 151–7.
Casari, G., Sander, C., et al. (1995). A method to predict functional residues in proteins. Nat Struct Biol 2(2): 171–8.
David, L., Luo, R., et al. (2001). Ligand-receptor docking with the Mining Minima optimizer. J Comput-Aided Mol Des 15: 157–71.
Dror, O., Benyamini, H., et al. (2003). MASS: multiple structural alignment by secondary structures. Bioinformatics 19Suppl 1: I95–I104.
Ewing, T.J.A. and I.D. Kuntz (1997). Critical evaluation of search algorithms for automated molecular docking and database screening. J Comp Chem 18: 1175–89.
Fariselli, P., Pazos, F., et al. (2002). Prediction of protein—protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 269(5): 1356–61.
Fetrow, J.S., Siew, N., et al. (2001). Genomic-scale comparison of sequence-and structure-based methods of function prediction: does structure provide additional insight? Protein Sci 10(5): 1005–14.
Gabb, H.A., Jackson, R.M., et al. (1997). Modeling protein docking using shape complementary, electrostatics, and biochemical information. J Mol Biol 272: 106–20.
Gerstein, M. and Levitt, M. (1996). Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. Proc Int Conf Intell Syst Mol Biol 4: 59–67.
Gibrat, J.F., Madej, T., et al. (1996). Surprising similarities in structure comparison. Curr Opin Struct Biol 6(3): 377–85.
Goh, C.S., Bogan, A.A., et al. (2000). Co-evolution of proteins with their interaction partners. J Mol Biol 299(2): 283–93.
Gough, J., Karplus, K., et al. (2001). Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313(4): 903–19.
Guener, O., Ed. (2000). Pharmacophore Perception, Developement, and Use in Drug Design. La Jolla, CA, International University Line USA.
Halperin, I., Ma, B., et al. (2002). Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47(4): 409–43.
Hansch, C., Leo, A., et al. (1995). Exploring QSAR. New York, Oxford University Press USA.
Hegyi, H. and Gerstein, M. (1999). The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 288(1): 147–64.
Hendlich, M. (1998). Databases for protein-ligand complexes. Acta Crystallogr D 54: 1178–82.
Holm, L. and Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J Mol Biol 233(1): 123–38.
Holm, L. and Sander, C. (1994). Parser for protein folding units. Proteins 19(3): 256–68.
Holm, L. and Sander, C. (1998). Dictionary of Recurrent Domains in Protein Structures. Proteins 1998(33): 88–96.
Hoy J et al. (2003). “A global representation of protein fold space” Proc. Nat. Acad. Sci.:100; 2386–2390.
Janin, J., Henrick, K., et al. (2003). CAPRI: a critical assessment of predicted interactions. Proteins 52: 2–9.
Jones, D. T. and Ward, J. J. (2003). Prediction of Disordered Regions in Proteins From Position Specific Score Matrices. Proteins 53: 573–578.
Katchalski-Katzir, Shariv, E., I., et al. (1992). Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 89: 2195–9.
Kinch, L. N., Wrabl, J. O., et al. (2003). CASP5 assessment of fold recognition target predictions. Proteins 53: 395–409.
Kobayashi, N. and Go, N. (1997). A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur Biophys J 126(2): 135–44.
Kuntz, I. D., Blaney, J. M., et al. (1982). A geometric approach to macromolecular-ligand interactions. J Mol Biol 161: 269–88.
Laskowski, R.A., Luscombe, N. M., et al. (1996). Protein clefts in molecular recognition and function. Protein Sci 5(12): 2438–52.
Lauri, G. and P.A. Barlett (1994). CAVEAT: a program to faciliate the design of organic molecules. J Comput-Aided Mol Des 8(1): 51–66.
Lawrence, M. C. and Davis, P. C. (1992). CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. Proteins 12: 31–41.
Leach, A. R. (1997). A survey of methods for searching the conformational space of small and medium-sized molecules. New York, Wiley-VCH.
Leach, A. R. (2001). Molecular Modeling: Principles and Applications. Englewood Cliffs, NJ, Prentice Hall.
Leach, A.R. and Hann, M.M. (2000). The in silico world of virtual libraries. Drug Discovery Today 5(8): 326–36.
Leibowitz, N., Nussinov, R., et al. (2001). MUSTA—a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. J Comput Biol 8(2): 93–121.
Lesk, A. M. and Chothia, C. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136(3): 225–70.
Levitt, M. and Chothia, C. (1976). Structural patterns in globular proteins. Nature 261(5561): 552–8.
Lichtarge, O., Bourne, H.R., et al. (1996). An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257(2): 342–58.
Liu, M. and Wang, S. M. (1999). MCDOCK: A Monte Carlo simulation approach to the molecular docking problem. J Comput-Aided Mol Des 13(5): 435–51.
Marchler-Bauer, A., Anderson, J. B., et al. (2003). CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 31(1): 383–7.
Marcotte, E. M., Pellegrini, M., et al. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428): 751–3.
Melamud, E. and Moult, J. (2003). Evaluation of disorder preditions in CASP5. Proteins 53: 561–565.
Morris, G.M., Goodsell, D. S., et al. (1998). Automated docking using a lamarckian genetic algorithm and an impirical binding free energy function. J Comp Chem 19: 1639–62.
Moult, J., Fidelis, K., et al. (2003). Critical Assessment of Methods of Protein Structure Prediction (CASP)-Round V. Proteins 53: 334–339.
Murzin, A. G., Brenner, S. E., et al. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247(4): 536–40.
Nooren, I. M. and Thornton, J. M. (2003). Diversity of protein-protein interactions. Embo J 22(14): 3486–92.
Obradovic, Z., Peng, K., et al. (2003). Predicting Intrinsic Disorder From Amino Acid Sequence. Proteins.
Orengo, C. A., Michie, A. D., et al. (1997). CATH—a hierarchic classification of protein domain structures. Structure 5(8): 1093–108.
Orengo, C. A., Pearl, et al. (2003). The CATH Domain Structure Database. Structural Bioinformatincs. P. E. Bourne and H. Weissig, Willey & Sons publication: 249–272.
Overbeek, R., Fonstein, M., et al. (1999). Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1(2): 93–108.
Pazos, F., Helmer-Citterich, M., et al. (1997). Correlated mutations contain information about protein-protein interaction. J Mol Biol 271(4): 511–23.
Pazos, F. and Valencia, A. (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14(9): 609–14.
Pellegrini, M., Marcotte, E. M., et al. (1999). Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96(8): 4285–8.
Pereira-Leal, J.B. and Seabra, M. C. (2001). Evolution of the Rab family of small GTP-binding proteins. J Mol Biol 313(4): 889–901.
Ragan, M. A. and Gaasterland, T. (1998). Microbial genescapes: a prokaryotic view of the yeast genome. Microb Comp Genomics 3(4): 219–35.
Rayer, M., Wefing, S., et al. (1996). Placement of medium-sized molecular fragments into active sites of proteins. 10: 41–54.
Russell, R. B. (1998). Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 279(5): 1211–27.
Rutenber, E., Fauman, E. B., et al. (1993). Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. J Biol Chem 268(21): 15343–6.
Sali, A. and Blundell, T. L. (1990). Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 212(2): 403–28.
Sandak, B., Wolfson, H. J., et al. (1998). Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers. Proteins 32: 159–74.
Schultz, J., Milpetz, F., et al. (1998). SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95(11): 5857–64.
Shatsky, M., Nussinov, R., et al. (2002). MultiProt-aMultiple Protein Structural Alignment Algorithm. Workshop on algorithms in bioinformatics, Springer Verlag. 2452: 235–250.
Shatsky, M., Nussinov, R., et al. (2002). Flexible protein alignment and hinge detection. Proteins 48(2): 242–56.
Shindyalov, I. N. and Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11(9): 739–47.
Shindyalov, I. N. and Bourne, P. E. (2001). A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res 29(1): 228–9.
Siddiqui, A. S. and Barton, G. J. (1995). Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci 4(5): 872–84.
Simons, K. T., Kooperberg, C., et al. (1997). Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268(1): 209–25.
Smith, G. R. and Sternberg, M. J. (2002). Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12(1): 28–35.
Sowdhamini, R., Burke, D. F., et al. (1998). Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies. Acta Crystallogr D Biol Crystallogr 54(Pt 6 Pt 1): 1168–77.
Su, A. I., Lorber, D. M., et al. (2001). Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins 42: 279–93.
Sun, Y., T. J. A. Ewing, et al. (1998). CombiDOCK: structure-based combinatorial docking and library design. J Comput-Aided Mol Des 12: 597–604.
Tamames, J., Casari, G., et al. (1997). Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44(1): 66–73.
Taylor, W. R. and Orengo, C. A. (1989). Protein structure alignment. J Mol Biol 208(1): 1–22.
Tramontano, A. and Morea, V. (2003). Assessment of homology-based predictions in CASP5. Proteins 53: 352–368.
Vakser, I.A. (1995). Protein docking for low-resolution structures. Protein Eng 8: 371–7.
Welch, W., Ruppert, J., et al. (1996). HAMMERHEAD: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3: 449–63.
Williams, N. (1997). Bioinformatics: how to get databases talking the same language. Science 275: 301–2.
Ye, Y. and Godzik, A. (2003). Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19Suppl 2: II246–II255.
Zhou, H.X. and Shan, Y. (2001). Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44(3): 336–43.
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Zhang, Q., Veretnik, S., Bourne, P.E. (2005). Overview of Structural Bioinformatics. In: Chen, YP.P. (eds) Bioinformatics Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26888-X_2
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