Skip to main content

Overview of Structural Bioinformatics

  • Chapter
Bioinformatics Technologies

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Aloyand, P. and Russell, R.B. (2003). InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19(1): 161–162.

    Google Scholar 

  • Aloy, P., Stark, A., et al. (2003). Predictions without templates: new folds, secondary structure, and contacts in CASP5. proteins 53: 436–456.

    Article  Google Scholar 

  • Bateman, A., Coin, L., et al. (2004). The Pfam protein families database. Nucleic Acids Res 32Database issue: D138–41.

    Google Scholar 

  • Berman, H.M., Westbrook, J., et al. (2000). The Protein Data Bank. Nucleic Acids Res 28(1): 235–42.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Bourne, P.E. (1999). Bioinformatics 15: 715–6.

    Google Scholar 

  • 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.

    Google Scholar 

  • Bourne, P.E., Berman, H.M., et al. (1997). The macromolecular Crystallographic Information File (mmCIF).

    Google Scholar 

  • Bourne, P.E. and Weissig, H. Eds. (2003). Structural Bioinformatics. Hoboken, NJ, Wiley-Liss, Inc.

    Google Scholar 

  • Burley, S.K., Almo, S.C., et al. (1999). Structural genomics: beyond the human genome project. Nat Genet 23: 151–7.

    Article  Google Scholar 

  • Casari, G., Sander, C., et al. (1995). A method to predict functional residues in proteins. Nat Struct Biol 2(2): 171–8.

    Article  Google Scholar 

  • David, L., Luo, R., et al. (2001). Ligand-receptor docking with the Mining Minima optimizer. J Comput-Aided Mol Des 15: 157–71.

    Google Scholar 

  • Dror, O., Benyamini, H., et al. (2003). MASS: multiple structural alignment by secondary structures. Bioinformatics 19Suppl 1: I95–I104.

    Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Gibrat, J.F., Madej, T., et al. (1996). Surprising similarities in structure comparison. Curr Opin Struct Biol 6(3): 377–85.

    Article  Google Scholar 

  • Goh, C.S., Bogan, A.A., et al. (2000). Co-evolution of proteins with their interaction partners. J Mol Biol 299(2): 283–93.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Guener, O., Ed. (2000). Pharmacophore Perception, Developement, and Use in Drug Design. La Jolla, CA, International University Line USA.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Hansch, C., Leo, A., et al. (1995). Exploring QSAR. New York, Oxford University Press USA.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Hendlich, M. (1998). Databases for protein-ligand complexes. Acta Crystallogr D 54: 1178–82.

    Article  Google Scholar 

  • Holm, L. and Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J Mol Biol 233(1): 123–38.

    Article  Google Scholar 

  • Holm, L. and Sander, C. (1994). Parser for protein folding units. Proteins 19(3): 256–68.

    Google Scholar 

  • Holm, L. and Sander, C. (1998). Dictionary of Recurrent Domains in Protein Structures. Proteins 1998(33): 88–96.

    Google Scholar 

  • Hoy J et al. (2003). “A global representation of protein fold space” Proc. Nat. Acad. Sci.:100; 2386–2390.

    Google Scholar 

  • Janin, J., Henrick, K., et al. (2003). CAPRI: a critical assessment of predicted interactions. Proteins 52: 2–9.

    Google Scholar 

  • Jones, D. T. and Ward, J. J. (2003). Prediction of Disordered Regions in Proteins From Position Specific Score Matrices. Proteins 53: 573–578.

    Google Scholar 

  • 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.

    Google Scholar 

  • Kinch, L. N., Wrabl, J. O., et al. (2003). CASP5 assessment of fold recognition target predictions. Proteins 53: 395–409.

    Google Scholar 

  • 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.

    Google Scholar 

  • Kuntz, I. D., Blaney, J. M., et al. (1982). A geometric approach to macromolecular-ligand interactions. J Mol Biol 161: 269–88.

    Article  Google Scholar 

  • Laskowski, R.A., Luscombe, N. M., et al. (1996). Protein clefts in molecular recognition and function. Protein Sci 5(12): 2438–52.

    Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Leach, A. R. (1997). A survey of methods for searching the conformational space of small and medium-sized molecules. New York, Wiley-VCH.

    Google Scholar 

  • Leach, A. R. (2001). Molecular Modeling: Principles and Applications. Englewood Cliffs, NJ, Prentice Hall.

    Google Scholar 

  • Leach, A.R. and Hann, M.M. (2000). The in silico world of virtual libraries. Drug Discovery Today 5(8): 326–36.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Levitt, M. and Chothia, C. (1976). Structural patterns in globular proteins. Nature 261(5561): 552–8.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Marcotte, E. M., Pellegrini, M., et al. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428): 751–3.

    Article  Google Scholar 

  • Melamud, E. and Moult, J. (2003). Evaluation of disorder preditions in CASP5. Proteins 53: 561–565.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Moult, J., Fidelis, K., et al. (2003). Critical Assessment of Methods of Protein Structure Prediction (CASP)-Round V. Proteins 53: 334–339.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Nooren, I. M. and Thornton, J. M. (2003). Diversity of protein-protein interactions. Embo J 22(14): 3486–92.

    Article  Google Scholar 

  • Obradovic, Z., Peng, K., et al. (2003). Predicting Intrinsic Disorder From Amino Acid Sequence. Proteins.

    Google Scholar 

  • Orengo, C. A., Michie, A. D., et al. (1997). CATH—a hierarchic classification of protein domain structures. Structure 5(8): 1093–108.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Overbeek, R., Fonstein, M., et al. (1999). Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1(2): 93–108.

    Google Scholar 

  • Pazos, F., Helmer-Citterich, M., et al. (1997). Correlated mutations contain information about protein-protein interaction. J Mol Biol 271(4): 511–23.

    Article  Google Scholar 

  • Pazos, F. and Valencia, A. (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14(9): 609–14.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Ragan, M. A. and Gaasterland, T. (1998). Microbial genescapes: a prokaryotic view of the yeast genome. Microb Comp Genomics 3(4): 219–35.

    Google Scholar 

  • Rayer, M., Wefing, S., et al. (1996). Placement of medium-sized molecular fragments into active sites of proteins. 10: 41–54.

    Google Scholar 

  • Russell, R. B. (1998). Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol 279(5): 1211–27.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Shatsky, M., Nussinov, R., et al. (2002). MultiProt-aMultiple Protein Structural Alignment Algorithm. Workshop on algorithms in bioinformatics, Springer Verlag. 2452: 235–250.

    Google Scholar 

  • Shatsky, M., Nussinov, R., et al. (2002). Flexible protein alignment and hinge detection. Proteins 48(2): 242–56.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Smith, G. R. and Sternberg, M. J. (2002). Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12(1): 28–35.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Tamames, J., Casari, G., et al. (1997). Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol 44(1): 66–73.

    Google Scholar 

  • Taylor, W. R. and Orengo, C. A. (1989). Protein structure alignment. J Mol Biol 208(1): 1–22.

    Article  Google Scholar 

  • Tramontano, A. and Morea, V. (2003). Assessment of homology-based predictions in CASP5. Proteins 53: 352–368.

    Article  Google Scholar 

  • Vakser, I.A. (1995). Protein docking for low-resolution structures. Protein Eng 8: 371–7.

    Article  Google Scholar 

  • Welch, W., Ruppert, J., et al. (1996). HAMMERHEAD: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3: 449–63.

    Article  Google Scholar 

  • Williams, N. (1997). Bioinformatics: how to get databases talking the same language. Science 275: 301–2.

    Google Scholar 

  • Ye, Y. and Godzik, A. (2003). Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19Suppl 2: II246–II255.

    Google Scholar 

  • Zhou, H.X. and Shan, Y. (2001). Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44(3): 336–43.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Hiedelberg

About this chapter

Cite this chapter

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

Download citation

  • DOI: https://doi.org/10.1007/3-540-26888-X_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20873-0

  • Online ISBN: 978-3-540-26888-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics