TY - JOUR AU - Koehl, P. PY - 2001 DA - 2001// TI - Protein structure similarities JO - Curr Opin Struct Biol VL - 11 UR - https://doi.org/10.1016/S0959-440X(00)00214-1 DO - 10.1016/S0959-440X(00)00214-1 ID - Koehl2001 ER - TY - JOUR AU - Sierk, M. L. AU - Pearson, W. R. PY - 2004 DA - 2004// TI - Sensitivity and selectivity in protein structure comparison JO - Protein Sci VL - 13 UR - https://doi.org/10.1110/ps.03328504 DO - 10.1110/ps.03328504 ID - Sierk2004 ER - TY - JOUR AU - Kolodny, R. AU - Koehl, P. AU - Levitt, M. PY - 2005 DA - 2005// TI - Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures JO - J Mol Biol VL - 346 UR - https://doi.org/10.1016/j.jmb.2004.12.032 DO - 10.1016/j.jmb.2004.12.032 ID - Kolodny2005 ER - TY - JOUR AU - Mizuguchi, K. AU - Go, N. PY - 1995 DA - 1995// TI - Seeking significance in three-dimensional protein structure comparisons JO - Curr Opin Struct Biol VL - 5 UR - https://doi.org/10.1016/0959-440X(95)80100-6 DO - 10.1016/0959-440X(95)80100-6 ID - Mizuguchi1995 ER - TY - JOUR AU - Yang, A. S. AU - Honig, B. PY - 2000 DA - 2000// TI - An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance JO - J Mol Biol VL - 301 UR - https://doi.org/10.1006/jmbi.2000.3973 DO - 10.1006/jmbi.2000.3973 ID - Yang2000 ER - TY - JOUR AU - Shapiro, J. AU - Brutlag, D. PY - 2004 DA - 2004// TI - FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh389 DO - 10.1093/nar/gkh389 ID - Shapiro2004 ER - TY - JOUR AU - May, A. C. PY - 1999 DA - 1999// TI - Toward more meaningful hierarchical classification of protein three-dimensional structures JO - Proteins VL - 37 UR - https://doi.org/3.0.CO;2-V DO - 3.0.CO;2-V ID - May1999 ER - TY - JOUR AU - Orengo, C. A. AU - Michie, A. D. AU - Jones, S. AU - Jones, D. T. AU - Swindells, M. B. AU - Thornton, J. M. PY - 1997 DA - 1997// TI - CATH--a hierarchic classification of protein domain structures JO - Structure VL - 5 UR - https://doi.org/10.1016/S0969-2126(97)00260-8 DO - 10.1016/S0969-2126(97)00260-8 ID - Orengo1997 ER - TY - JOUR AU - Matsuo, Y. AU - Bryant, S. H. PY - 1999 DA - 1999// TI - identification of homologous core structures. JO - Proteins VL - 35 UR - https://doi.org/3.0.CO;2-9 DO - 3.0.CO;2-9 ID - Matsuo1999 ER - TY - JOUR AU - Dietmann, S. AU - Holm, L. PY - 2001 DA - 2001// TI - Identification of homology in protein structure classification JO - Nat Struct Biol VL - 8 UR - https://doi.org/10.1038/nsb1101-953 DO - 10.1038/nsb1101-953 ID - Dietmann2001 ER - TY - JOUR AU - Dietmann, S. AU - Fernandez-Fuentes, N. AU - Holm, L. PY - 2002 DA - 2002// TI - Automated detection of remote homology JO - Curr Opin Struct Biol VL - 12 UR - https://doi.org/10.1016/S0959-440X(02)00332-9 DO - 10.1016/S0959-440X(02)00332-9 ID - Dietmann2002 ER - TY - JOUR AU - Kawabata, T. AU - Nishikawa, K. PY - 2000 DA - 2000// TI - Protein structure comparison using the markov transition model of evolution JO - Proteins VL - 41 UR - https://doi.org/3.0.CO;2-S DO - 3.0.CO;2-S ID - Kawabata2000 ER - TY - JOUR AU - Holm, L. AU - Sander, C. PY - 1997 DA - 1997// TI - Decision support system for the evolutionary classification of protein structures JO - Proc Int Conf Intell Syst Mol Biol VL - 5 ID - Holm1997 ER - TY - JOUR AU - Russell, R. B. AU - Barton, G. J. PY - 1994 DA - 1994// TI - Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility JO - J Mol Biol VL - 244 UR - https://doi.org/10.1006/jmbi.1994.1733 DO - 10.1006/jmbi.1994.1733 ID - Russell1994 ER - TY - JOUR AU - Yang, A. S. AU - Honig, B. PY - 2000 DA - 2000// TI - An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence JO - J Mol Biol VL - 301 UR - https://doi.org/10.1006/jmbi.2000.3974 DO - 10.1006/jmbi.2000.3974 ID - Yang2000 ER - TY - JOUR AU - Panchenko, A. R. AU - Wolf, Y. I. AU - Panchenko, L. A. AU - Madej, T. PY - 2005 DA - 2005// TI - Evolutionary plasticity of protein families: coupling between sequence and structure variation JO - Proteins VL - 61 UR - https://doi.org/10.1002/prot.20644 DO - 10.1002/prot.20644 ID - Panchenko2005 ER - TY - JOUR AU - Murzin, A. G. AU - Brenner, S. E. AU - Hubbard, T. AU - Chothia, C. PY - 1995 DA - 1995// TI - SCOP: a structural classification of proteins database for the investigation of sequences and structures JO - J Mol Biol VL - 247 ID - Murzin1995 ER - TY - JOUR AU - Gibrat, J. F. AU - Madej, T. AU - Bryant, S. H. PY - 1996 DA - 1996// TI - Surprising similarities in structure comparison JO - Curr Opin Struct Biol VL - 6 UR - https://doi.org/10.1016/S0959-440X(96)80058-3 DO - 10.1016/S0959-440X(96)80058-3 ID - Gibrat1996 ER - TY - JOUR AU - Panchenko, A. R. AU - Madej, T. PY - 2004 DA - 2004// TI - Analysis of protein homology by assessing the (dis)similarity in protein loop regions JO - Proteins VL - 57 UR - https://doi.org/10.1002/prot.20237 DO - 10.1002/prot.20237 ID - Panchenko2004 ER - TY - JOUR AU - Ponting, C. P. AU - Russell, R. B. PY - 2000 DA - 2000// TI - Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins JO - J Mol Biol VL - 302 UR - https://doi.org/10.1006/jmbi.2000.4087 DO - 10.1006/jmbi.2000.4087 ID - Ponting2000 ER - TY - JOUR AU - Copley, R. R. AU - Bork, P. PY - 2000 DA - 2000// TI - Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways JO - J Mol Biol VL - 303 UR - https://doi.org/10.1006/jmbi.2000.4152 DO - 10.1006/jmbi.2000.4152 ID - Copley2000 ER - TY - STD TI - Supplementary data url for HCS paper.. [http://www.ncbi.nlm.nih.gov/Structure/madej/hcs_tables.htm] UR - http://www.ncbi.nlm.nih.gov/Structure/madej/hcs_tables.htm ID - ref22 ER - TY - JOUR AU - Carpentier, M. AU - Brouillet, S. AU - Pothier, J. PY - 2005 DA - 2005// TI - YAKUSA: a fast structural database scanning method JO - Proteins VL - 61 UR - https://doi.org/10.1002/prot.20517 DO - 10.1002/prot.20517 ID - Carpentier2005 ER - TY - JOUR AU - Hou, J. AU - Jun, S. R. AU - Zhang, C. AU - Kim, S. H. PY - 2005 DA - 2005// TI - Global mapping of the protein structure space and application in structure-based inference of protein function JO - Proceedings of the National Academy of Sciences of the United States of America VL - 102 UR - https://doi.org/10.1073/pnas.0409772102 DO - 10.1073/pnas.0409772102 ID - Hou2005 ER - TY - JOUR AU - Sam, V. AU - Tai, C. H. AU - Garnier, J. AU - Gibrat, J. F. AU - Lee, B. AU - Munson, P. J. PY - 2006 DA - 2006// TI - ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification JO - BMC bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-206 DO - 10.1186/1471-2105-7-206 ID - Sam2006 ER - TY - JOUR AU - Marchler-Bauer, A. AU - Anderson, J. B. AU - DeWeese-Scott, C. AU - Fedorova, N. D. AU - Geer, L. Y. AU - He, S. AU - Hurwitz, D. I. AU - Jackson, J. D. AU - Jacobs, A. R. AU - Lanczycki, C. J. AU - Liebert, C. A. AU - Liu, C. AU - Madej, T. AU - Marchler, G. H. AU - Mazumder, R. AU - Nikolskaya, A. N. AU - Panchenko, A. R. AU - Rao, B. S. AU - Shoemaker, B. A. AU - Simonyan, V. AU - Song, J. S. AU - Thiessen, P. A. AU - Vasudevan, S. AU - Wang, Y. AU - Yamashita, R. A. AU - Yin, J. J. AU - Bryant, S. H. PY - 2003 DA - 2003// TI - CDD: a curated Entrez database of conserved domain alignments JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg087 DO - 10.1093/nar/gkg087 ID - Marchler-Bauer2003 ER - TY - JOUR AU - Marchler-Bauer, A. AU - Panchenko, A. R. AU - Shoemaker, B. A. AU - Thiessen, P. A. AU - Geer, L. Y. AU - Bryant, S. H. PY - 2002 DA - 2002// TI - CDD: a database of conserved domain alignments with links to domain three-dimensional structure JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.281 DO - 10.1093/nar/30.1.281 ID - Marchler-Bauer2002 ER - TY - STD TI - Website url for Conserved Domains Database.. [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml] UR - http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml ID - ref28 ER - TY - JOUR AU - Chen, J. AU - Anderson, J. B. AU - DeWeese-Scott, C. AU - Fedorova, N. D. AU - Geer, L. Y. AU - He, S. AU - Hurwitz, D. I. AU - Jackson, J. D. AU - Jacobs, A. R. AU - Lanczycki, C. J. AU - Liebert, C. A. AU - Liu, C. AU - Madej, T. AU - Marchler-Bauer, A. AU - Marchler, G. H. AU - Mazumder, R. AU - Nikolskaya, A. N. AU - Rao, B. S. AU - Panchenko, A. R. AU - Shoemaker, B. A. AU - Simonyan, V. AU - Song, J. S. AU - Thiessen, P. A. AU - Vasudevan, S. AU - Wang, Y. AU - Yamashita, R. A. AU - Yin, J. J. AU - Bryant, S. H. PY - 2003 DA - 2003// TI - MMDB: Entrez's 3D-structure database JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg086 DO - 10.1093/nar/gkg086 ID - Chen2003 ER - TY - STD TI - Another supplementary data url for HCS paper.. [http://www.ncbi.nlm.nih.gov/Structure/madej/structmeasures05.htm] UR - http://www.ncbi.nlm.nih.gov/Structure/madej/structmeasures05.htm ID - ref30 ER - TY - JOUR AU - McLachlan, A. D. PY - 1979 DA - 1979// TI - Gene duplications in the structural evolution of chymotrypsin JO - J Mol Biol VL - 128 UR - https://doi.org/10.1016/0022-2836(79)90308-5 DO - 10.1016/0022-2836(79)90308-5 ID - McLachlan1979 ER - TY - STD TI - Link to Structure home page.. [http://www.ncbi.nlm.nih.gov/Structure/] UR - http://www.ncbi.nlm.nih.gov/Structure/ ID - ref32 ER - TY - STD TI - URL for VAST Search web server.. [http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html] UR - http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html ID - ref33 ER -