Recognition of Functional Sites in Protein Structures☆

[1]  Honorine Nocon,et al.  In the press … , 1907, California state journal of medicine.

[2]  Thomas S. Huang,et al.  Image processing , 1971 .

[3]  C. Bron,et al.  Algorithm 457: finding all cliques of an undirected graph , 1973 .

[4]  Coenraad Bron,et al.  Finding all cliques of an undirected graph , 1973 .

[5]  Julian R. Ullmann,et al.  An Algorithm for Subgraph Isomorphism , 1976, J. ACM.

[6]  W. Kabsch.  A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .

[7]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[8]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

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

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

[11]  M. L. Connolly.  Measurement of protein surface shape by solid angles , 1986 .

[12]  George C. Stockman,et al.  Object recognition and localization via pose clustering , 1987, Comput. Vis. Graph. Image Process..

[13]  Yehezkel Lamdan,et al.  Geometric Hashing: A General And Efficient Model-based Recognition Scheme , 1988, [1988 Proceedings] Second International Conference on Computer Vision.

[14]  H. Wolfson,et al.  Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[15]  D Fischer,et al.  A computer vision based technique for 3-D sequence-independent structural comparison of proteins. , 1993, Protein engineering.

[16]  P. Willett,et al.  A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. , 1994, Journal of molecular biology.

[17]  E.E. Pissaloux,et al.  Image Processing , 1994, Proceedings. Second Euromicro Workshop on Parallel and Distributed Processing.

[18]  D Fischer,et al.  Molecular surface representations by sparse critical points , 1994, Proteins.

[19]  T. A. Jones,et al.  Lipid-binding proteins: a family of fatty acid and retinoid transport proteins. , 1994, Advances in protein chemistry.

[20]  Gerhard Sagerer,et al.  Segmentation of molecular surfaces based on their convex hull , 1995, Proceedings., International Conference on Image Processing.

[21]  G. Schulz,et al.  High‐resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer , 1995, Protein science : a publication of the Protein Society.

[22]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[23]  Kurt Mehlhorn,et al.  LEDA: a platform for combinatorial and geometric computing , 1997, CACM.

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

[25]  M. Masuya,et al.  Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations. , 1995, Journal of molecular graphics.

[26]  R. Nussinov,et al.  Molecular recognition via face center representation of a molecular surface. , 1996, Journal of Molecular Graphics.

[27]  J. Thornton,et al.  Protein recognition of adenylate: an example of a fuzzy recognition template. , 1996, Journal of molecular biology.

[28]  J M Thornton,et al.  Derivation of 3D coordinate templates for searching structural databases: Application to ser‐His‐Asp catalytic triads in the serine proteinases and lipases , 1996, Protein science : a publication of the Protein Society.

[29]  Boris Steipe,et al.  Metric properties of the root-mean-square deviation of vector sets , 1997 .

[30]  L. Banaszak,et al.  The Crystal Structure of the Liver Fatty Acid-binding Protein , 1997, The Journal of Biological Chemistry.

[31]  Haim J. Wolfson,et al.  Geometric hashing: an overview , 1997 .

[32]  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.

[33]  B Chevrier,et al.  The structure of Staphylococcus aureus epidermolytic toxin A, an atypic serine protease, at 1.7 A resolution. , 1997, Structure.

[34]  S. Kim,et al.  Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[35]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[36]  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.

[37]  R. Nussinov,et al.  Molecular shape comparisons in searches for active sites and functional similarity. , 1998, Protein engineering.

[38]  Christian Lemmen,et al.  Computational methods for the structural alignment of molecules , 2000, J. Comput. Aided Mol. Des..

[39]  Yunje Cho,et al.  Structure-based identification of a novel NTPase from Methanococcus jannaschii , 1999, Nature Structural Biology.

[40]  C. Hill,et al.  Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani , 1999, The EMBO journal.

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

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

[43]  J C Sacchettini,et al.  Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein. , 2000, The Journal of biological chemistry.

[44]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[45]  William R. Taylor,et al.  Structure Comparison and Structure Patterns , 2000, J. Comput. Biol..

[46]  K. Denessiouk,et al.  Adenine recognition: A motif present in ATP‐, CoA‐, NAD‐, NADP‐, and FAD‐dependent proteins , 2001, Proteins.

[47]  Kohei Oda,et al.  Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes , 2001, Nature Structural Biology.

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

[49]  T. Langer,et al.  Virtual screening: an effective tool for lead structure discovery? , 2001, Current pharmaceutical design.

[50]  Patrice Koehl,et al.  ASTRAL compendium enhancements , 2002, Nucleic Acids Res..

[51]  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.

[52]  Ruth Nussinov,et al.  Efficient Unbound Docking of Rigid Molecules , 2002, WABI.

[53]  Ruth Nussinov,et al.  MultiProt - A Multiple Protein Structural Alignment Algorithm , 2002, WABI.

[54]  G. Klebe,et al.  A new method to detect related function among proteins independent of sequence and fold homology. , 2002, Journal of molecular biology.

[55]  H. Wolfson,et al.  Multiple diverse ligands binding at a single protein site : A matter of pre-existing populations , 2001 .

[56]  Jonathan W. Essex,et al.  A review of protein-small molecule docking methods , 2002, J. Comput. Aided Mol. Des..

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

[58]  Gerhard Klebe,et al.  Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. , 2003, Journal of molecular biology.

[59]  Jie Liang,et al.  Inferring functional relationships of proteins from local sequence and spatial surface patterns. , 2003, Journal of molecular biology.

[60]  K. Kinoshita,et al.  Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site , 2003, Protein science : a publication of the Protein Society.

[61]  Rolf Hilgenfeld,et al.  Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs , 2003, Science.

[62]  Ruth Nussinov,et al.  Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. , 2003, Current medicinal chemistry.

[63]  G. Gao,et al.  The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Yosef Y. Kuttner,et al.  A consensus‐binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine‐containing complexes , 2003, Proteins.

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

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

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

[68]  Ruth Nussinov,et al.  A method for simultaneous alignment of multiple protein structures , 2004, Proteins.

[69]  Ruth Nussinov,et al.  Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. , 2004, Current medicinal chemistry.

[70]  K. Kinoshita,et al.  Identification of protein functions from a molecular surface database, eF-site , 2004, Journal of Structural and Functional Genomics.

[71]  Patrice Koehl,et al.  The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..

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

[73]  Ruth Nussinov,et al.  BioInfo3D: a suite of tools for structural bioinformatics , 2004, Nucleic Acids Res..

[74]  Lila M Gierasch,et al.  Sequence and structural analysis of cellular retinoic acid‐binding proteins reveals a network of conserved hydrophobic interactions , 2003, Proteins.

[75]  Rita Casadio,et al.  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.