Resources and Infrastructure for Structural Bioinformatics

  • Dong Xu
  • Jie Liang
  • Ying Xu
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)


In the past decade, hundreds of computational tools and databases have been developed and deployed in support of protein structure prediction and modeling by the computational structural biology community. The majority of these tools and databases have been made freely available to the general public through the Internet. Many of the computational tools are accessible in the form of computational servers, supported by powerful high-performance computers, making them just fingertips away for protein researchers in any corner of the world. Other tools have been made freely downloadable so they can be run on users’ local computers. Some of the databases, such as Protein Data Bank (PDB; Bernstein et al., 1977; Deshpande et al., 2005) and SCOP (Murzin et al., 1995), as well as tools such as RasMol (Sayle and Milner-White, 1995), PHD (Rost et al., 1994) and CE (Shindyalov and Bourne, 1998), have made profound impacts on biological science in general, having become indispensable in the daily research and development activities in many biological research labs. As the field continues to attract researchers from other scientific disciplines, including computer science, mathematics, statistics, physics, and chemistry, we expect that more reliable, efficient, and easy-to-use tools and databases will be introduced at an even higher rate than in the past decade.


Protein Structure Prediction Nuclear Magnetic Reso Virtual Reality Modeling Language Protein Secondary Structure Prediction Structural Bioinformatics 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Altman, R.B., and Dugan, J.M. 2003. Defining bioinformatics and structural bioinformatics. Methods Biochem. Anal. 44:3–14.Google Scholar
  2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402.CrossRefGoogle Scholar
  3. Attwood, T.K., Flower, D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., Scordis, P., Selley, J., and Wright, W. 1999. PRINTS prepares for the new millennium. Nucleic Acids Res. 27:220–225.CrossRefGoogle Scholar
  4. Bairoch, A. 1993. The ENZYME data bank. Nucleic Acids Res. 21:3155–3156.CrossRefGoogle Scholar
  5. Bairoch, A., and Apweiler, R. 1999. The SwissProt protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 27:49–54.CrossRefGoogle Scholar
  6. Barker, W.C., Garavelli, J.S., McGarvey, P.B., Marzec, C.R., Orcutt, B.C., Srinivasarao, G.Y., Yeh, L.L., Ledley, R.S., Mewes, H., Pfeiffer, F., Tsugita, A., and Wu, C. 1999. The PIR-international protein sequence database. Nucleic Acids Res. 27:39–42.CrossRefGoogle Scholar
  7. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, F.D., and Sonnhammer, E.L.L. 1999. Pfam 3.1: 1313 multiple alignments match the majority of proteins. Nucleic Acids Res. 27:260–262.CrossRefGoogle Scholar
  8. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, and B.A., Wheeler, D.L. 2000. GenBank. Nucleic Acids Res. 28:15–18.CrossRefGoogle Scholar
  9. 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 structures. J. Mol. Biol. 112:535–542.CrossRefGoogle Scholar
  10. Binkowski, T.A., Adamian, L., and Liang, J. 2003. Inferring functional relationships of proteins from local sequence and spatial surface patterns. J. Mol. Biol. 332:505–526.CrossRefGoogle Scholar
  11. Bourne, P., Berman, H., Watenpaugh, K., Westbrook, J., and Fitzgerald, P. 1997. The macromolecular crystallographic information file (mmCIF). Methods Enzymol. 277:571–590.CrossRefGoogle Scholar
  12. Bourne, P.E. and Weissig, H. (eds.). 2003. Structural Bioinformatics (Methods of Biochemical Analysis, Vol. 44). New York, John Wiley & Sons.Google Scholar
  13. Chen, L., Oughtred, R., Berman, H.M., and Westbrook, J. 2004. TargetDB: A target registration database for structural genomics projects. Bioinformatics 20:2860–2862.CrossRefGoogle Scholar
  14. Chou, K.C. 2004. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11:2105–2134.Google Scholar
  15. Corpet, F., Gouzy, J., and Kahn, D. 1999. Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res. 27:263–267.CrossRefGoogle Scholar
  16. Deshpande, N., Addess, K.J., Bluhm, W.F., Merino-Ott, J.C., Townsend-Merino, W, Zhang, Q., Knezevich, C., Xie, L., Chen, L., Feng, Z., Kramer Green, R., Flippen-Anderson, J.L., Westbrook, J., Berman, H.M., and Bourne, P.E. 2005. The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33(Suppl.l): D233–D237.Google Scholar
  17. Echols, N., Milburn, D., and Gerstein, M. 2003. MolMovDB: Analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31:478–482.CrossRefGoogle Scholar
  18. Etzold, T., Ulyanov, A., and Argos, P. 1996. SRS: Information retrieval system for molecular biology data banks. Methods Enzymol. 266:114–128.CrossRefGoogle Scholar
  19. Fauman, E.B., Hopkins, A.L., and Groom, C.R. 2003. Structural bioinformatics in drug discovery. Methods Biochem. Anal. 44:477–497.Google Scholar
  20. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., and Ben-Tal, N. 2003.ConSurf: Identification of functional regions in proteins by surfacemapping of phylogenetic information. Bioinformatics 19:163–164.CrossRefGoogle Scholar
  21. Guex, N., and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714–2723.CrossRefGoogle Scholar
  22. Henikoff, S., and Henikoff, J.G. 1991. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19:6565–6572.CrossRefGoogle Scholar
  23. Higgins, D., and Taylor, W. (eds.). 2000. Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach. London, Oxford University Press.Google Scholar
  24. Hofmann, K., Bucher, P., Falquet, L., and Bairoch, A. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:215–219.CrossRefGoogle Scholar
  25. Holm, L., and Sander, C. 1998. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26:316–319.CrossRefGoogle Scholar
  26. Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD: Visual molecular dynamics. J. Mol. Graph. 14:33–38.CrossRefGoogle Scholar
  27. Jiang, T., Xu, Y., and Zhang, M. (eds.). 2002. Current Topics in Computational Molecular Biology. Cambridge, MA, MIT Press.Google Scholar
  28. Kanehisa, M., and Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28:27–30.CrossRefGoogle Scholar
  29. Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946–950.CrossRefGoogle Scholar
  30. Laskowski, R.A., Hutchinson, E.G., Michie, A.D., Wallace, A.C., Jones, M.L., and Thornton, J.M. 1997. PDBsum: A web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci. 22:488–190.CrossRefGoogle Scholar
  31. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283–291.CrossRefGoogle Scholar
  32. Liang, J., Edelsbrunner, H., and Woodward, C. 1998. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci. 7:1884–1897.CrossRefGoogle Scholar
  33. Marchler-Bauer, A., Addess, K.J., Chappey, C., Geer, L., Madej, T., Matsuo, Y., Wang, Y., and Bryant, S.H. 1999. MMDB: Entrez’s 3D structure database. Nucleic Acids Res. 27:240–243.CrossRefGoogle Scholar
  34. Michalopoulos, I., Torrance, G.M., Gilbert, D.R., and Westhead, D.R. 2004. TOPS: An enhanced database of protein structural topology. Nucleic Acid Res. 32:D251–D254.CrossRefGoogle Scholar
  35. Murvai, J., Vlahovicek, K., Barta, E., Szepesvari, C., Acatrinei, C., and Pongor, S. 1999. The SBASE protein domain library, release 6.0: A collection of annotated protein sequence segments. Nucleic Acids Res. 27:257–259.CrossRefGoogle Scholar
  36. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536–540.Google Scholar
  37. Nayal, M., Hitz, B.C., and Honig, B. 1999. GRASS: A server for the graphical representation and analysis of structures. Protein Sci. 8:676–679.CrossRefGoogle Scholar
  38. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH—A hierarchic classification of protein domain structures. Structure 5:1093–1108.CrossRefGoogle Scholar
  39. Pegg, S.C.-H., Brown, S., Ojha, S., Huang, C.C., Ferrin, T.E. and Babbitt, P.C. 2005. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac. Symp. Biocomput. pp. 260–271. World Scientific Publishing.Google Scholar
  40. Porter, C.T., Bartlett, G.J., and Thornton, J.M. 2004. The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 32: D129–D133.CrossRefGoogle Scholar
  41. Rost, B., Sander, C., and Schneider, R. 1994. PHD—an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:53–60.Google Scholar
  42. Sanner, M.F. 1999. Python: A programming language for software integration and development. J. Mol. Graph. Mod. 17:57–61.Google Scholar
  43. Sanner, M.F., Duncan, B.S., Carrillo, C.J., and Olson, A.J. 1999. Integrating computation and visualization for biomolecular analysis: An example using Python and AVS. Proc. Pac. Symp. Biocomput.’ 99, pp. 401–412.Google Scholar
  44. Sayle, R.A., and Milner-White, E.J. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20:374.CrossRefGoogle Scholar
  45. Schuler, G.D., Epstein, J.A., Ohkawa, H., and Kans, J.A. 1996. Entrez: Molecular biology database and retrieval system. Methods Enzymol. 266:141–162.CrossRefGoogle Scholar
  46. Shindyalov, I.N., and Bourne, P.E. 1995. WPDB: A PC-based tool for analyzing protein structure. J. Appl. Crystallogr. 28:847–852.CrossRefGoogle Scholar
  47. Shindyalov, I.N., and Bourne, P.E. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:739–747.CrossRefGoogle Scholar
  48. Shnel, J. 1996. Image library of biological macromolecules. Comput. Appl. Biosci. 12:227–229.Google Scholar
  49. 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. 4:872–884.CrossRefGoogle Scholar
  50. Tate, J.G., Moreland, J., and Bourne, P.E. 2001. Design and implementation of a collaborative molecular graphics environment. J. Mol. Graph. Model. 19(3-4):280–287, 369–373.CrossRefGoogle Scholar
  51. Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278:631–637.CrossRefADSGoogle Scholar
  52. The Gene Ontology Consortium. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32: D258–D261.CrossRefGoogle Scholar
  53. Tsigelny, I. (ed.). 2002. Protein Structure Prediction: Bioinformatic Approach. La Jolla, CA, International University Line Publishers, pp. 5–41.Google Scholar
  54. University of Wisconsin. 1999. BioMagResBank. Madison, University of Wisconsin.Google Scholar
  55. Vriend, G. 1990. WHAT IF: A molecular modelling and drug design program. J. Mol. Graph. 8:52–56.CrossRefGoogle Scholar
  56. Wallace, A.C., Laskowski, R.A., and Thornton, J.M. 1996. Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5:1001–1013.CrossRefGoogle Scholar
  57. Webster, D.M. 2000. Protein Structure Prediction: Methods and Protocols. Totowa, NJ, Humana Press.CrossRefGoogle Scholar
  58. Wolfson, H.J., Shatsky, M., Schneidman-Duhovny, D., Dror, O., Shulman-Peleg, A., Ma, B., and Nussinov, R. 2005. From structure to function: Methods and applications. Curr. Protein Pept. Sci. 6:171–183.CrossRefGoogle Scholar
  59. Xu, D., Xu, Y., and Uberbacher, E.C. 2000. Computational tools for protein modeling. Curr. Protein Pept. Sci. 1:1–21.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Dong Xu
    • 1
  • Jie Liang
    • 2
  • Ying Xu
    • 3
  1. 1.Computer Science DepartmentUniversity of Missouri-ColumbiaColumbia
  2. 2.Department of BioengineeringUniversity of Illinois at ChicagoChicago
  3. 3.Institute of Bioinformatics and Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthens

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