Literature References

Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., & Murzin, A. G. (2004). SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res, 32 Database issue, D226-229.

Berman, H., Henrick, K., Nakamura, H., & Markley, J. L. (2007). The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res, 35(Database issue), D301-303.

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. (2000). The Protein Data Bank. Nucleic Acids Res, 28(1), 235-242.

Bhat, T. N., Bourne, P., Feng, Z., Gilliland, G., Jain, S., Ravichandran, V., et al. (2001). The PDB data uniformity project. Nucleic Acids Res, 29(1), 214-218.

Bhattacharya, S., Bhattacharyya, C., & Chandra, N. R. (2006). Projections for fast protein structure retrieval. BMC Bioinformatics, 7 Suppl 5, S5.

Binkowski, T. A., Naghibzadeh, S., & Liang, J. (2003). CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res, 31(13), 3352-3355.

Bourne, P. E., Addess, K. J., Bluhm, W. F., Chen, L., Deshpande, N., Feng, Z., et al. (2004). The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res, 32(Database issue), D223-225.

Burkhardt, K., Schneider, B., & Ory, J. (2006). A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PLoS Comput Biol, 2(10), e99.

Camoglu, O., Kahveci, T., & Singh, A. K. (2003). Towards index-based similarity search for protein structure databases. Proc IEEE Comput Soc Bioinform Conf, 2, 148-158.

Chen, J., Anderson, J. B., DeWeese-Scott, C., Fedorova, N. D., Geer, L. Y., He, S., et al. (2003). MMDB: Entrez's 3D-structure database. Nucleic Acids Res, 31(1), 474-477.

Chu, C. K., Feng, L. L., & Wouters, M. A. (2005). Comparison of sequence and structure-based datasets for nonredundant structural data mining. Proteins, 60(4), 577-583.

Daras, P., Zarpalas, D., Axenopoulos, A., Tzovaras, D., & Strintzis, M. G. (2006). Three-dimensional shape-structure comparison method for protein classification. IEEE/ACM Trans Comput Biol Bioinform, 3(3), 193-207.

Day, R., Beck, D. A., Armen, R. S., & Daggett, V. (2003). A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci, 12(10), 2150-2160.

Deshpande, N., Addess, K. J., Bluhm, W. F., Merino-Ott, J. C., Townsend-Merino, W., Zhang, Q., et al. (2005). The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res, 33(Database issue), D233-237.

Ferre, F., Ausiello, G., Zanzoni, A., & Helmer-Citterich, M. (2004). SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res, 32(Database issue), D240-244.

Frishman, D., Albermann, K., Hani, J., Heumann, K., Metanomski, A., Zollner, A., et al. (2001). Functional and structural genomics using PEDANT. Bioinformatics, 17(1), 44-57.

Frishman, D., Mokrejs, M., Kosykh, D., Kastenmuller, G., Kolesov, G., Zubrzycki, I., et al. (2003). The PEDANT genome database. Nucleic Acids Res, 31(1), 207-211.

Fulton, K. F., Bate, M. A., Faux, N. G., Mahmood, K., Betts, C., & Buckle, A. M. (2007). Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. Nucleic Acids Res, 35(Database issue), D304-307.

Garcia-Serna, R., Opatowski, L., & Mestres, J. (2006). FCP: functional coverage of the proteome by structures. Bioinformatics, 22(14), 1792-1793.

Gewehr, J. E., Hintermair, V., & Zimmer, R. (2007). AutoSCOP: automated prediction of SCOP classifications using unique\ pattern-class mappings. Bioinformatics\, 23\(10\), 1203-1210\.

Gough, J. (2002). The SUPERFAMILY database in structural genomics. Acta Crystallogr D Biol Crystallogr, 58(Pt 11), 1897-1900.

Gough, J., & Chothia, C. (2002). SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res, 30(1), 268-272.

Greene, L. H., Lewis, T. E., Addou, S., Cuff, A., Dallman, T., Dibley, M., et al. (2007). The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res, 35(Database issue), D291-297.

Hubbard, T. J., Ailey, B., Brenner, S. E., Murzin, A. G., & Chothia, C. (1998). SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D Biol Crystallogr, 54(Pt 6 Pt 1), 1147-1154.

Hubbard, T. J., Murzin, A. G., Brenner, S. E., & Chothia, C. (1997). SCOP: a structural classification of proteins database. Nucleic Acids Res, 25(1), 236-239.

Kolesov, G., Virnau, P., Kardar, M., & Mirny, L. A. (2007). Protein knot server: detection of knots in protein structures. Nucleic Acids Res, 35(Web Server issue), W425-428.

Kouranov, A., Xie, L., de la Cruz, J., Chen, L., Westbrook, J., Bourne, P. E., et al. (2006). The RCSB PDB information portal for structural genomics. Nucleic Acids Res, 34(Database issue), D302-305.

Lai, Y. L., Yen, S. C., Yu, S. H., & Hwang, J. K. (2007). pKNOT: the protein KNOT web server. Nucleic Acids Res, 35(Web Server issue), W420-424.

Laskowski, R. A., Chistyakov, V. V., & Thornton, J. M. (2005). PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res, 33(Database issue), D266-268.

Le Gall, T., Romero, P. R., Cortese, M. S., Uversky, V. N., & Dunker, A. K. (2007). Intrinsic disorder in the Protein Data Bank. J Biomol Struct Dyn, 24(4), 325-342.

Levitt, M. (2007). Growth of novel protein structural data. Proc Natl Acad Sci U S A, 104(9), 3183-3188.

Lo Conte, L., Ailey, B., Hubbard, T. J., Brenner, S. E., Murzin, A. G., & Chothia, C. (2000). SCOP: a structural classification of proteins database. Nucleic Acids Res, 28(1), 257-259.

Lo Conte, L., Brenner, S. E., Hubbard, T. J., Chothia, C., & Murzin, A. G. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res, 30(1), 264-267.

Marchler-Bauer, A., Anderson, J. B., Derbyshire, M. K., DeWeese-Scott, C., Gonzales, N. R., Gwadz, M., et al. (2007). CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res, 35(Database issue), D237-240.

McGuffin, L. J., Street, S. A., Bryson, K., Sorensen, S. A., & Jones, D. T. (2004). The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res, 32(Database issue), D196-199.

Michalopoulos, I., Torrance, G. M., Gilbert, D. R., & Westhead, D. R. (2004). TOPS: an enhanced database of protein structural topology. Nucleic Acids Res, 32(Database issue), D251-254.

Pieper, U., Eswar, N., Braberg, H., Madhusudhan, M. S., Davis, F. P., Stuart, A. C., et al. (2004). MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res, 32(Database issue), D217-222.

Prlic, A., Down, T. A., & Hubbard, T. J. (2005). Adding some SPICE to DAS. Bioinformatics, 21 Suppl 2, ii40-41.

Reeves, G. A., Dallman, T. J., Redfern, O. C., Akpor, A., & Orengo, C. A. (2006). Structural diversity of domain superfamilies in the CATH database. J Mol Biol, 360(3), 725-741.

Rother, K., Michalsky, E., & Leser, U. (2005). How well are protein structures annotated in secondary databases? Proteins, 60(4), 571-576.

Schlessinger, A., Ofran, Y., Yachdav, G., & Rost, B. (2006). Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res, 34(Database issue), D777-780.

Sheik, S. S., Sundararajan, P., Hussain, A. S., & Sekar, K. (2002). Ramachandran plot on the web. Bioinformatics, 18(11), 1548-1549.

Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., et al. (2007). DisProt: the Database of Disordered Proteins. Nucleic Acids Res, 35(Database issue), D786-793.

Sridhar, S., Babu, A. V., & Guruprasad, K. (2007). PSSARD (2.0): a database server for making flexible queries relating amino acid sequences to main-chain secondary structure conformations for proteins of known three-dimensional structure and certain useful applications. Int J Biol Macromol, 41(1), 109-113.

Stebbings, L. A., & Mizuguchi, K. (2004). HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res, 32(Database issue), D203-207.

Szustakowski, J. D., Kasif, S., & Weng, Z. (2005). Less is more: towards an optimal universal description of protein folds. Bioinformatics, 21 Suppl 2, ii66-71.

Tsien, C. L., Libermann, T. A., Gu, X., & Kohane, I. S. (2001). On reporting fold differences. Pac Symp Biocomput, 496-507.

Tung, C. H., & Yang, J. M. (2007). fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Res, 35(Web Server issue), W438-443.

Tusnady, G. E., Dosztanyi, Z., & Simon, I. (2005). PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res, 33(Database issue), D275-278.

Vucetic, S., Obradovic, Z., Vacic, V., Radivojac, P., Peng, K., Iakoucheva, L. M., et al. (2005). DisProt: a database of protein disorder. Bioinformatics, 21(1), 137-140.

Wang, Y., Addess, K. J., Chen, J., Geer, L. Y., He, J., He, S., et al. (2007). MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res, 35(Database issue), D298-300.

Westbrook, J., Feng, Z., Chen, L., Yang, H., & Berman, H. M. (2003). The Protein Data Bank and structural genomics. Nucleic Acids Res, 31(1), 489-491.

Westbrook, J., Feng, Z., Jain, S., Bhat, T. N., Thanki, N., Ravichandran, V., et al. (2002). The Protein Data Bank: unifying the archive. Nucleic Acids Res, 30(1), 245-248.

Westbrook, J., Ito, N., Nakamura, H., Henrick, K., & Berman, H. M. (2005). PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics, 21(7), 988-992.

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., et al. (2007). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 35(Database issue), D5-12.

Wilson, D., Madera, M., Vogel, C., Chothia, C., & Gough, J. (2007). The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res, 35(Database issue), D308-313.

Yang, J. M., & Tung, C. H. (2006). Protein structure database search and evolutionary classification. Nucleic Acids Res, 34(13), 3646-3659.