Protein structure based prediction of catalytic residues
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[1] Gil Amitai,et al. Network analysis of protein structures identifies functional residues. , 2004, Journal of molecular biology.
[2] Ronald J. Williams,et al. Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves , 2005, Proteins.
[3] B. Rost,et al. Protein structures sustain evolutionary drift. , 1997, Folding & design.
[4] John D. Westbrook,et al. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods , 2011, Journal of Structural and Functional Genomics.
[5] Ashish V. Tendulkar,et al. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. , 2003, Journal of molecular biology.
[6] A. Valencia. Automatic annotation of protein function. , 2005, Current opinion in structural biology.
[7] C. Sander,et al. Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases , 1993, Protein science : a publication of the Protein Society.
[8] Thomas L. Madden,et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.
[9] Ruth Nussinov,et al. Triggering loops and enzyme function: identification of loops that trigger and modulate movements. , 2003, Journal of molecular biology.
[10] András Fiser,et al. Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation , 1996, FEBS letters.
[11] Jaime Prilusky,et al. Automated analysis of interatomic contacts in proteins , 1999, Bioinform..
[12] J. Thornton,et al. Missing in action: enzyme functional annotations in biological databases. , 2009, Nature chemical biology.
[13] Ying Wei,et al. Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties , 2009, PLoS Comput. Biol..
[14] V. Schramm,et al. Enzymatic transition states and dynamic motion in barrier crossing. , 2009, Nature chemical biology.
[15] Michael Lappe,et al. Detection of protein catalytic residues at high precision using local network properties , 2008, BMC Bioinformatics.
[16] Gail J. Bartlett,et al. Analysis of catalytic residues in enzyme active sites. , 2002, Journal of molecular biology.
[17] Itay Mayrose,et al. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues , 2002, ISMB.
[18] Annabel E. Todd,et al. Evolution of function in protein superfamilies, from a structural perspective. , 2001, Journal of molecular biology.
[19] Stephen K Burley,et al. Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein. , 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.
[20] Cathy H. Wu,et al. Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties , 2006, BMC Bioinformatics.
[21] H. Edelsbrunner,et al. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.
[22] P. Radivojac,et al. Evaluation of features for catalytic residue prediction in novel folds , 2007 .
[23] Robert B Russell,et al. A model for statistical significance of local similarities in structure. , 2003, Journal of molecular biology.
[24] Kimmen Sjölander,et al. INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification , 2008, Bioinform..
[25] Mallur S. Madhusudhan,et al. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins , 2011, Nucleic Acids Res..
[26] Kai Wang,et al. Incorporating background frequency improves entropy-based residue conservation measures , 2006, BMC Bioinform..
[27] B. Rost. Enzyme function less conserved than anticipated. , 2002, Journal of molecular biology.
[28] R. Ranganathan,et al. Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.
[29] M. Eisenstein,et al. Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces. , 2005, Journal of molecular biology.
[30] András Fiser,et al. MMM: a sequence-to-structure alignment protocol , 2006, Bioinform..
[31] Fredrik Johansson,et al. A comparative study of conservation and variation scores , 2010, BMC Bioinformatics.
[32] Sophie Sacquin-Mora,et al. Locating the active sites of enzymes using mechanical properties , 2007, Proteins.
[33] Leszek Rychlewski,et al. FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..
[34] Geoffrey E. Hinton,et al. Learning representations by back-propagating errors , 1986, Nature.
[35] Jodi Basner,et al. Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis. , 2006, Chemical reviews.
[36] Patricia C. Babbitt,et al. Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies , 2009, PLoS Comput. Biol..
[37] Lukasz A. Kurgan,et al. Accurate sequence-based prediction of catalytic residues , 2008, Bioinform..
[38] Ian Sillitoe,et al. FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies , 2011, Nucleic Acids Res..
[39] Adam Godzik,et al. Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..
[40] Mona Singh,et al. Predicting functionally important residues from sequence conservation , 2007, Bioinform..
[41] Walter R. Gilks,et al. Modeling the percolation of annotation errors in a database of protein sequences , 2002, Bioinform..
[42] Janet M. Thornton,et al. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis , 2003, Bioinform..
[43] Gabriel del Rio,et al. Improved prediction of critical residues for protein function based on network and phylogenetic analyses , 2005, BMC Bioinformatics.
[44] Andrea Passerini,et al. Automatic prediction of catalytic residues by modeling residue structural neighborhood , 2010, BMC Bioinformatics.
[45] F. Cohen,et al. An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.
[46] Johannes Söding,et al. Prediction of protein functional residues from sequence by probability density estimation , 2008, Bioinform..
[47] Mike P. Liang,et al. Structural characterization of proteins using residue environments , 2005, Proteins.
[48] Johannes Söding,et al. HHsenser: exhaustive transitive profile search using HMM–HMM comparison , 2006, Nucleic Acids Res..
[49] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[50] Sergey Brin,et al. The Anatomy of a Large-Scale Hypertextual Web Search Engine , 1998, Comput. Networks.
[51] Janet M. Thornton,et al. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data , 2004, Nucleic Acids Res..
[52] Peter B. McGarvey,et al. UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..
[53] A. Fiser,et al. The ybeY protein from Escherichia coli is a metalloprotein. , 2005, Acta crystallographica. Section F, Structural biology and crystallization communications.