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.

[1]  Linus Pauling,et al.  Molecular Architecture and Biological Reactions , 1946 .

[2]  L. Pauling,et al.  Nature of Forces between Large Molecules of Biological Interest , 1948, Nature.

[3]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[4]  J. Janin,et al.  Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.

[5]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[6]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[7]  P. Srere,et al.  Why are enzymes so big , 1984 .

[8]  G. Rose,et al.  Molecular cartography of globular proteins with application to antigenic sites , 1986, Biopolymers.

[9]  A M Lesk,et al.  Interior and surface of monomeric proteins. , 1987, Journal of molecular biology.

[10]  H. Kawasaki,et al.  Molecular cloning of the cDNA for the large subunit of the high-Ca2+-requiring form of human Ca2+-activated neutral protease. , 1988, Biochemistry.

[11]  I. Kuntz,et al.  Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. , 1988, Journal of medicinal chemistry.

[12]  M J Sternberg,et al.  Analysis and prediction of the location of catalytic residues in enzymes. , 1988, Protein engineering.

[13]  T. Hynes,et al.  Transfer of a β-turn structure to a new protein context , 1989, Nature.

[14]  Y. Satow,et al.  Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. , 1990, Science.

[15]  S. Kanaya,et al.  Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis. , 1990, The Journal of biological chemistry.

[16]  H. Wolfson,et al.  An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. , 1992, Journal of biomolecular structure & dynamics.

[17]  D. Levitt,et al.  POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. , 1992, Journal of molecular graphics.

[18]  M Wilmanns,et al.  Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution. , 1992, Journal of molecular biology.

[19]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[20]  R. Fletterick,et al.  Catalysis and regulationProteases , 1992 .

[21]  D. Ringe,et al.  Modularity of protein function: chimeric interleukin 1 beta s containing specific protease inhibitor loops retain function of both molecules. , 1993, Biochemistry.

[22]  W. Lipscomb,et al.  X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state. , 1993, Biochemistry.

[23]  A shifting specificity model for enzyme catalysis. , 1993, Journal of theoretical biology.

[24]  A. Bairoch.  The ENZYME data bank. , 1993, Nucleic acids research.

[25]  L. L. Lloyd,et al.  Enzyme nomenclature — Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology: Academic Press Ltd, London, UK, 1992. xiii + 862 pp. Price £40.00. ISBN 0-12-227165-3 , 1994 .

[26]  Ann M Stock,et al.  Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB. , 1995, Journal of molecular biology.

[27]  R. Laskowski.  SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.

[28]  Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR. , 1995, Journal of molecular biology.

[29]  Jeffrey W. Smith,et al.  Protein Loop Grafting to Construct a Variant of Tissue-type Plasminogen Activator That Binds Platelet Integrin αIIbβ3(*) , 1995, The Journal of Biological Chemistry.

[30]  Ruth Nussinov,et al.  An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching , 1995, Comput. Appl. Biosci..

[31]  D. Ringe.  What makes a binding site a binding site? , 1995, Current opinion in structural biology.

[32]  M. Swindells,et al.  Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.

[33]  C. Frömmel,et al.  The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. , 1996, Journal of molecular biology.

[34]  W. Guida,et al.  The art and practice of structure‐based drug design: A molecular modeling perspective , 1996, Medicinal research reviews.

[35]  Y. Hu,et al.  Crystal structure of glycine N-methyltransferase from rat liver. , 1996, Biochemistry.

[36]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[37]  D. Benjamin,et al.  Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies. , 1996, Journal of molecular biology.

[38]  C. Vita,et al.  Changing the Structural Context of a Functional -Hairpin , 1996, The Journal of Biological Chemistry.

[39]  C. Vita.  Engineering novel proteins by transfer of active sites to natural scaffolds. , 1997, Current opinion in biotechnology.

[40]  R E Hubbard,et al.  Can drugs be designed? , 1997, Current opinion in biotechnology.

[41]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[42]  Tim J. P. Hubbard,et al.  SCOP: a structural classification of proteins database , 1998, Nucleic Acids Res..

[43]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[44]  For enzymes, bigger is better. , 1997, Biophysical chemistry.

[45]  J. Thornton,et al.  Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites , 1997, Protein science : a publication of the Protein Society.

[46]  M Hendlich,et al.  LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.

[47]  Fang Wang,et al.  Hydrogen exchange/electrospray ionization mass spectrometry studies of substrate and inhibitor binding and conformational changes of Escherichia coli dihydrodipicolinate reductase. , 1997, Biochemistry.

[48]  P. Nordlund,et al.  Crystal structure of common type acylphosphatase from bovine testis. , 1997, Structure.

[49]  Ann M Stock,et al.  Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[50]  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.

[51]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[52]  C. Orengo,et al.  Evolution of protein function, from a structural perspective. , 1999, Current opinion in chemical biology.

[53]  A. Sali,et al.  Structural genomics: beyond the Human Genome Project , 1999, Nature Genetics.

[54]  G J Kleywegt,et al.  Recognition of spatial motifs in protein structures. , 1999, Journal of molecular biology.

[55]  M. Gerstein,et al.  The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. , 1999, Journal of molecular biology.

[56]  W. Gmeiner,et al.  Hydrogen exchange shows peptide binding stabilizes motions in Hck SH2. , 1999, Biochemistry.

[57]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[58]  I. Luque,et al.  Structural stability of binding sites: Consequences for binding affinity and allosteric effects , 2000, Proteins.

[59]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[60]  Gerhard Klebe,et al.  Recent developments in structure-based drug design , 2000, Journal of Molecular Medicine.

[61]  R. Huber,et al.  The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[62]  James E. Bray,et al.  Assigning genomic sequences to CATH , 2000, Nucleic Acids Res..

[63]  P. Dean,et al.  Recent advances in structure-based rational drug design. , 2000, Current opinion in structural biology.

[64]  Annabel E. Todd,et al.  From structure to function: Approaches and limitations , 2000, Nature Structural Biology.

[65]  T. Hitchens,et al.  Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. , 2000, Biochemistry.

[66]  S. Henikoff,et al.  Blocks‐based methods for detecting protein homology , 2000, Electrophoresis.

[67]  M. Sternberg,et al.  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. , 2001, Journal of molecular biology.

[68]  J. Thornton,et al.  The (βα)8 glycosidases: sequence and structure analyses suggest distant evolutionary relationships , 2001 .

[69]  N. Ben-Tal,et al.  ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.

[70]  K. Ramnarayan,et al.  Recent developments in computational proteomics. , 2001, Drug discovery today.

[71]  M. Ondrechen,et al.  THEMATICS: A simple computational predictor of enzyme function from structure , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[72]  D. Eisenberg,et al.  Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. , 2001, Journal of molecular biology.

[73]  Liisa Holm,et al.  Identification of homology in protein structure classification , 2001, Nature Structural Biology.

[74]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

[75]  A. Elcock.  Prediction of functionally important residues based solely on the computed energetics of protein structure. , 2001, Journal of molecular biology.

[76]  Raghavan Varadarajan,et al.  A Procedure for Detection and Quantitation of Cavity Volumes in Proteins , 2002, The Journal of Biological Chemistry.

[77]  C. Orengo,et al.  One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. , 2002, Journal of molecular biology.

[78]  Gail J. Bartlett,et al.  Analysis of catalytic residues in enzyme active sites. , 2002, Journal of molecular biology.

[79]  Miriam Eisenstein,et al.  Electrostatics in protein–protein docking , 2002, Protein science : a publication of the Protein Society.

[80]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[81]  G. Phillips,et al.  Dynamics of proteins in crystals: comparison of experiment with simple models. , 2002, Biophysical journal.

[82]  Gail J. Bartlett,et al.  Using a neural network and spatial clustering to predict the location of active sites in enzymes. , 2003, Journal of molecular biology.

[83]  M. Jambon,et al.  A new bioinformatic approach to detect common 3D sites in protein structures , 2003, Proteins.

[84]  Robert B Russell,et al.  A model for statistical significance of local similarities in structure. , 2003, Journal of molecular biology.

[85]  Karl H. Clodfelter,et al.  Identification of substrate binding sites in enzymes by computational solvent mapping. , 2003, Journal of molecular biology.

[86]  Gail J. Bartlett,et al.  Catalysing new reactions during evolution: economy of residues and mechanism. , 2003, Journal of molecular biology.

[87]  K. Nishikawa,et al.  Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. , 2003, Journal of molecular biology.

[88]  Miriam Eisenstein,et al.  Weighted geometric docking: Incorporating external information in the rotation‐translation scan , 2003, Proteins.

[89]  L. Kavraki,et al.  An accurate, sensitive, and scalable method to identify functional sites in protein structures. , 2003, Journal of molecular biology.

[90]  S. J. Campbell,et al.  Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.

[91]  Janet M. Thornton,et al.  An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis , 2003, Bioinform..

[92]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[93]  Ashish V. Tendulkar,et al.  Functional sites in protein families uncovered via an objective and automated graph theoretic approach. , 2003, Journal of molecular biology.

[94]  Peter Willett,et al.  Searching for Patterns of Amino Acids in 3D Protein Structures , 2003, J. Chem. Inf. Comput. Sci..

[95]  Robert B Russell,et al.  Finding functional sites in structural genomics proteins. , 2004, Structure.

[96]  J. Warwicker,et al.  Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. , 2004, Journal of molecular biology.

[97]  Miriam Eisenstein,et al.  Hydrophobic complementarity in protein–protein docking , 2004, Proteins.

[98]  Miriam Eisenstein,et al.  On proteins, grids, correlations, and docking. , 2004, Comptes rendus biologies.

[99]  J. Thornton,et al.  Searching for functional sites in protein structures. , 2004, Current opinion in chemical biology.

[100]  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..

[101]  R. Raz,et al.  ProMate: a structure based prediction program to identify the location of protein-protein binding sites. , 2004, Journal of molecular biology.

[102]  Raghavan Varadarajan,et al.  Accurate detection of protein:ligand binding sites using molecular dynamics simulations. , 2004, Structure.

[103]  Dan S. Tawfik,et al.  Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes , 2004, Nature Structural &Molecular Biology.

[104]  Gil Amitai,et al.  Network analysis of protein structures identifies functional residues. , 2004, Journal of molecular biology.

[105]  A. Panchenko,et al.  Prediction of functional sites by analysis of sequence and structure conservation , 2004, Protein science : a publication of the Protein Society.

[106]  Alexandre M J J Bonvin,et al.  Data‐driven docking for the study of biomolecular complexes , 2005, The FEBS journal.

[107]  Ronald J. Williams,et al.  Statistical criteria for the identification of protein active sites using theoretical microscopic titration curves , 2005, Proteins.