TY - JOUR AU - Watson, J. D. AU - Laskowski, R. A. AU - Thornton, J. M. PY - 2005 DA - 2005// TI - Predicting protein function from sequence and structural data JO - Curr Opin Struct Biol VL - 15 UR - https://doi.org/10.1016/j.sbi.2005.04.003 DO - 10.1016/j.sbi.2005.04.003 ID - Watson2005 ER - TY - JOUR AU - Lichtarge, O. AU - Bourne, H. R. AU - Cohen, F. E. PY - 1996 DA - 1996// TI - An evolutionary trace method defines binding surfaces common to protein families JO - J Mol Biol VL - 257 UR - https://doi.org/10.1006/jmbi.1996.0167 DO - 10.1006/jmbi.1996.0167 ID - Lichtarge1996 ER - TY - JOUR AU - Landgraf, R. AU - Xenarios, I. AU - Eisenberg, D. PY - 2001 DA - 2001// TI - Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins JO - J Mol Biol VL - 307 UR - https://doi.org/10.1006/jmbi.2001.4540 DO - 10.1006/jmbi.2001.4540 ID - Landgraf2001 ER - TY - JOUR AU - Madabushi, S. AU - Yao, H. AU - Marsh, M. AU - Kristensen, D. M. AU - Philippi, A. AU - Sowa, M. E. AU - Lichtarge, O. PY - 2002 DA - 2002// TI - Structural clusters of evolutionary trace residues are statistically significant and common in proteins JO - J Mol Biol VL - 316 UR - https://doi.org/10.1006/jmbi.2001.5327 DO - 10.1006/jmbi.2001.5327 ID - Madabushi2002 ER - TY - JOUR AU - Glaser, F. AU - Pupko, T. AU - Paz, I. AU - Bell, R. E. AU - Bechor-Shental, D. AU - Martz, E. AU - Ben-Tal, N. PY - 2003 DA - 2003// TI - ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.1.163 DO - 10.1093/bioinformatics/19.1.163 ID - Glaser2003 ER - TY - JOUR AU - Chelliah, V. AU - Chen, L. AU - Blundell, T. L. AU - Lovell, S. C. PY - 2004 DA - 2004// TI - Distinguishing structural and functional restraints in evolution in order to identify interaction sites JO - J Mol Biol VL - 342 UR - https://doi.org/10.1016/j.jmb.2004.08.022 DO - 10.1016/j.jmb.2004.08.022 ID - Chelliah2004 ER - TY - JOUR AU - del Sol, A. AU - Pazos, F. AU - Valencia, A. PY - 2003 DA - 2003// TI - Automatic methods for predicting functionally important residues JO - J Mol Biol VL - 326 UR - https://doi.org/10.1016/S0022-2836(02)01451-1 DO - 10.1016/S0022-2836(02)01451-1 ID - del Sol2003 ER - TY - JOUR AU - Aloy, P. AU - Querol, E. AU - Aviles, F. X. AU - Sternberg, M. J. PY - 2001 DA - 2001// TI - Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking JO - J Mol Biol VL - 311 UR - https://doi.org/10.1006/jmbi.2001.4870 DO - 10.1006/jmbi.2001.4870 ID - Aloy2001 ER - TY - JOUR AU - Innis, C. A. AU - Anand, A. P. AU - Sowdhamini, R. PY - 2004 DA - 2004// TI - Prediction of functional sites in proteins using conserved functional group analysis JO - J Mol Biol VL - 337 UR - https://doi.org/10.1016/j.jmb.2004.01.053 DO - 10.1016/j.jmb.2004.01.053 ID - Innis2004 ER - TY - JOUR AU - Nimrod, G. AU - Glaser, F. AU - Steinberg, D. AU - Ben-Tal, N. AU - Pupko, T. PY - 2005 DA - 2005// TI - In silico identification of functional regions in proteins JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1023 DO - 10.1093/bioinformatics/bti1023 ID - Nimrod2005 ER - TY - JOUR AU - Nimrod, G. AU - Schushan, M. AU - Steinberg, D. M. AU - Ben-Tal, N. PY - 2008 DA - 2008// TI - Detection of functionally important regions in “hypothetical proteins” of known structure JO - Structure VL - 16 UR - https://doi.org/10.1016/j.str.2008.10.017 DO - 10.1016/j.str.2008.10.017 ID - Nimrod2008 ER - TY - JOUR AU - Mihalek, I. AU - Res, I. AU - Lichtarge, O. PY - 2006 DA - 2006// TI - Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins JO - Proteins VL - 63 UR - https://doi.org/10.1002/prot.20866 DO - 10.1002/prot.20866 ID - Mihalek2006 ER - TY - JOUR AU - Acharya, K. R. AU - Stuart, D. I. AU - Walker, N. P. AU - Lewis, M. AU - Phillips, D. C. PY - 1989 DA - 1989// TI - Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme JO - J Mol Biol VL - 208 UR - https://doi.org/10.1016/0022-2836(89)90091-0 DO - 10.1016/0022-2836(89)90091-0 ID - Acharya1989 ER - TY - JOUR AU - Callewaert, L. AU - Michiels, C. W. PY - 2010 DA - 2010// TI - Lysozymes in the animal kingdom JO - J Biosci VL - 35 UR - https://doi.org/10.1007/s12038-010-0015-5 DO - 10.1007/s12038-010-0015-5 ID - Callewaert2010 ER - TY - JOUR AU - Todd, A. E. AU - Orengo, C. A. AU - Thornton, J. M. PY - 2001 DA - 2001// TI - Evolution of function in protein superfamilies, from a structural perspective JO - J Mol Biol VL - 307 UR - https://doi.org/10.1006/jmbi.2001.4513 DO - 10.1006/jmbi.2001.4513 ID - Todd2001 ER - TY - JOUR AU - Rost, B. PY - 2002 DA - 2002// TI - Enzyme function less conserved than anticipated JO - J Mol Biol VL - 318 UR - https://doi.org/10.1016/S0022-2836(02)00016-5 DO - 10.1016/S0022-2836(02)00016-5 ID - Rost2002 ER - TY - JOUR AU - Mihalek, I. AU - Res, I. AU - Lichtarge, O. PY - 2006 DA - 2006// TI - A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti791 DO - 10.1093/bioinformatics/bti791 ID - Mihalek2006 ER - TY - JOUR AU - Mihalek, I. AU - Res, I. AU - Lichtarge, O. PY - 2004 DA - 2004// TI - A family of evolution-entropy hybrid methods for ranking protein residues by importance JO - J Mol Biol VL - 336 UR - https://doi.org/10.1016/j.jmb.2003.12.078 DO - 10.1016/j.jmb.2003.12.078 ID - Mihalek2004 ER - TY - BOOK AU - Haining, R. PY - 2003 DA - 2003// TI - Spatial Data Analysis -Theory and Practice- PB - Cambridge University Press CY - UK, Camabridge UR - https://doi.org/10.1017/CBO9780511754944 DO - 10.1017/CBO9780511754944 ID - Haining2003 ER - TY - JOUR AU - Levy, E. D. AU - Pereira-Leal, J. B. AU - Chothia, C. AU - Teichmann, S. A. PY - 2006 DA - 2006// TI - 3D complex: a structural classification of protein complexes JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020155 DO - 10.1371/journal.pcbi.0020155 ID - Levy2006 ER - TY - JOUR AU - Xu, Q. AU - Canutescu, A. AU - Obradovic, Z. AU - Dunbrack, R. L. PY - 2006 DA - 2006// TI - ProtBuD: a database of biological unit structures of protein families and superfamilies JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl490 DO - 10.1093/bioinformatics/btl490 ID - Xu2006 ER - TY - JOUR AU - Pruitt, K. D. AU - Tatusova, T. AU - Maglott, D. R. PY - 2007 DA - 2007// TI - NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl842 DO - 10.1093/nar/gkl842 ID - Pruitt2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Porter, C. T. AU - Bartlett, G. J. AU - Thornton, J. M. PY - 2004 DA - 2004// TI - The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh028 DO - 10.1093/nar/gkh028 ID - Porter2004 ER - TY - JOUR AU - Gore, S. P. AU - Burke, D. F. AU - Blundell, T. L. PY - 2005 DA - 2005// TI - PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti523 DO - 10.1093/bioinformatics/bti523 ID - Gore2005 ER - TY - JOUR AU - Bartlett, G. J. AU - Porter, C. T. AU - Borkakoti, N. AU - Thornton, J. M. PY - 2002 DA - 2002// TI - Analysis of catalytic residues in enzyme active sites JO - J Mol Biol VL - 324 UR - https://doi.org/10.1016/S0022-2836(02)01036-7 DO - 10.1016/S0022-2836(02)01036-7 ID - Bartlett2002 ER - TY - JOUR AU - Innis, C. A. AU - Shi, J. AU - Blundell, T. L. PY - 2000 DA - 2000// TI - Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis JO - Protein Eng VL - 13 UR - https://doi.org/10.1093/protein/13.12.839 DO - 10.1093/protein/13.12.839 ID - Innis2000 ER - TY - JOUR AU - Capra, J. A. AU - Laskowski, R. A. AU - Thornton, J. M. AU - Singh, M. AU - Funkhouser, T. A. PY - 2009 DA - 2009// TI - Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000585 DO - 10.1371/journal.pcbi.1000585 ID - Capra2009 ER - TY - JOUR AU - Petrova, N. V. AU - Wu, C. H. PY - 2006 DA - 2006// TI - Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-312 DO - 10.1186/1471-2105-7-312 ID - Petrova2006 ER - TY - JOUR AU - Moran, P. PY - 1948 DA - 1948// TI - The interpretation of statistical maps JO - Journal of the Royal Statistical Society VL - 10 ID - Moran1948 ER - TY - BOOK AU - Cliff, A. S. AU - Ord, J. K. PY - 1973 DA - 1973// TI - Spatial Autocorrelation PB - Pion CY - London ID - Cliff1973 ER - TY - BOOK AU - Fischer, M. AU - Scholten, H. AU - Unvin, D. PY - 1997 DA - 1997// TI - Spatial Analytial Perspectives on GIS in Environmental and Socio-economic Sciences PB - Francis CY - London ID - Fischer1997 ER - TY - CHAP AU - Anselin, L. ED - Fischer, M. ED - Scholten, H. ED - Unvin, D. PY - 1997 DA - 1997// TI - The Moran scatterplot as an ESDA tool to assess local instability in spatial association BT - Spatial Analytial Perspectives on GIS in Environmental and Socio-economic Sciences PB - Francis CY - London ID - Anselin1997 ER - TY - JOUR AU - Hwang, K. Y. AU - Baek, K. AU - Kim, H. Y. AU - Cho, Y. PY - 1998 DA - 1998// TI - The crystal structure of flap endonuclease-1 from Methanococcus jannaschii JO - Nat Struct Biol VL - 5 UR - https://doi.org/10.1038/1406 DO - 10.1038/1406 ID - Hwang1998 ER - TY - JOUR AU - Valdar, W. S. PY - 2002 DA - 2002// TI - Scoring residue conservation JO - Proteins VL - 48 UR - https://doi.org/10.1002/prot.10146 DO - 10.1002/prot.10146 ID - Valdar2002 ER - TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1992 DA - 1992// TI - Amino acid substitution matrices from protein blocks JO - Proc Natl Acad Sci U S A VL - 89 UR - https://doi.org/10.1073/pnas.89.22.10915 DO - 10.1073/pnas.89.22.10915 ID - Henikoff1992 ER - TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1994 DA - 1994// TI - Position-based sequence weights JO - J Mol Biol VL - 243 UR - https://doi.org/10.1016/0022-2836(94)90032-9 DO - 10.1016/0022-2836(94)90032-9 ID - Henikoff1994 ER - TY - JOUR AU - Katoh, K. AU - Toh, H. PY - 2008 DA - 2008// TI - Recent developments in the MAFFT multiple sequence alignment program JO - Brief Bioinform VL - 9 UR - https://doi.org/10.1093/bib/bbn013 DO - 10.1093/bib/bbn013 ID - Katoh2008 ER - TY - JOUR AU - Chelliah, V. AU - Blundell, T. AU - Mizuguchi, K. PY - 2005 DA - 2005// TI - Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition JO - Proteins VL - 61 UR - https://doi.org/10.1002/prot.20617 DO - 10.1002/prot.20617 ID - Chelliah2005 ER - TY - JOUR AU - Mazin, P. V. AU - Gelfand, M. S. AU - Mironov, A. A. AU - Rakhmaninova, A. B. AU - Rubinov, A. R. AU - Russell, R. B. AU - Kalinina, O. V. PY - 2010 DA - 2010// TI - An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies JO - Algorithms Mol Biol VL - 5 UR - https://doi.org/10.1186/1748-7188-5-29 DO - 10.1186/1748-7188-5-29 ID - Mazin2010 ER - TY - JOUR AU - Sander, C. AU - Schneider, R. PY - 1991 DA - 1991// TI - Database of homology-derived protein structures and the structural meaning of sequence alignment JO - Proteins VL - 9 UR - https://doi.org/10.1002/prot.340090107 DO - 10.1002/prot.340090107 ID - Sander1991 ER - TY - JOUR AU - Kouranov, A. AU - Xie, L. AU - de la Cruz, J. AU - Chen, L. AU - Westbrook, J. AU - Bourne, P. E. AU - Berman, H. M. PY - 2006 DA - 2006// TI - The RCSB PDB information portal for structural genomics JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj120 DO - 10.1093/nar/gkj120 ID - Kouranov2006 ER -