Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts.
暂无分享,去创建一个
[1] M J Sternberg,et al. Analysis and prediction of the location of catalytic residues in enzymes. , 1988, Protein engineering.
[2] S. Creighton,et al. Enzymes work by solvation substitution rather than by desolvation. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[3] C. Sander,et al. A method to predict functional residues in proteins , 1995, Nature Structural Biology.
[4] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[5] E. Fauman,et al. The X-ray Crystal Structures of Yersinia Tyrosine Phosphatase with Bound Tungstate and Nitrate , 1996, The Journal of Biological Chemistry.
[6] G. Cohen,et al. Interactions of protein antigens with antibodies. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[7] F. Cohen,et al. An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.
[8] N. Guex,et al. SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.
[9] R. Raines,et al. The CXXC motif: a rheostat in the active site. , 1997, Biochemistry.
[10] S. Benkovic,et al. Solvation, Reorganization Energy, and Biological Catalysis* , 1998, The Journal of Biological Chemistry.
[11] 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.
[12] A. Warshel. Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites* , 1998, The Journal of Biological Chemistry.
[13] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[14] R. Russell,et al. Analysis and prediction of functional sub-types from protein sequence alignments. , 2000, Journal of molecular biology.
[15] 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.
[16] 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.
[17] 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.
[18] R. Wolfenden,et al. The depth of chemical time and the power of enzymes as catalysts. , 2001, Accounts of chemical research.
[19] A. Elcock. Prediction of functionally important residues based solely on the computed energetics of protein structure. , 2001, Journal of molecular biology.
[20] Q. Wang,et al. Activation of human rhinovirus-14 3C protease. , 2001, Virology.
[21] Arend Sidow,et al. Inference of functional regions in proteins by quantification of evolutionary constraints , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[22] Gail J. Bartlett,et al. Analysis of catalytic residues in enzyme active sites. , 2002, Journal of molecular biology.
[23] B. Golinelli‐Pimpaneau. Structural diversity of antibody catalysts. , 2002, Journal of immunological methods.
[24] W. S. Valdar,et al. Scoring residue conservation , 2002, Proteins.
[25] Ganesh S Anand,et al. Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB. , 2002, Biochemistry.
[26] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[27] 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.
[28] J. Skolnick,et al. How well is enzyme function conserved as a function of pairwise sequence identity? , 2003, Journal of molecular biology.
[29] Nick V Grishin,et al. Using protein design for homology detection and active site searches , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[30] Janet M Thornton,et al. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. , 2003, Nucleic acids research.
[31] A. Warshel,et al. On the Generation of Catalytic Antibodies by Transition State Analogues , 2003, Chembiochem : a European journal of chemical biology.
[32] 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.
[33] Sung-Hou Kim,et al. Overview of structural genomics: from structure to function. , 2003, Current opinion in chemical biology.
[34] L. Kavraki,et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. , 2003, Journal of molecular biology.
[35] Yael Mandel-Gutfreund,et al. Annotating nucleic acid-binding function based on protein structure. , 2003, Journal of molecular biology.
[36] Kengo Kinoshita,et al. Protein informatics towards function identification. , 2003, Current opinion in structural biology.
[37] P. Dobson,et al. Distinguishing enzyme structures from non-enzymes without alignments. , 2003, Journal of molecular biology.
[38] Irene T Weber,et al. Analysis of protein structures reveals regions of rare backbone conformation at functional sites , 2003, Proteins.
[39] Janet M. Thornton,et al. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis , 2003, Bioinform..
[40] C. Anthony. The quinoprotein dehydrogenases for methanol and glucose. , 2004, Archives of biochemistry and biophysics.
[41] Yu-Dong Cai,et al. Prediction of protein function in the absence of significant sequence similarity. , 2004, Current medicinal chemistry.
[42] Kengo Kinoshita,et al. Structure‐based prediction of DNA‐binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces , 2004, Proteins.
[43] Igor Polikarpov,et al. Average protein density is a molecular‐weight‐dependent function , 2004, Protein science : a publication of the Protein Society.
[44] J. Warwicker,et al. Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. , 2004, Journal of molecular biology.
[45] Ihsan A. Shehadi,et al. Future directions in protein function prediction , 2002, Molecular Biology Reports.
[46] J. Thornton,et al. Searching for functional sites in protein structures. , 2004, Current opinion in chemical biology.
[47] 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..
[48] Jim Warwicker,et al. Improved pKa calculations through flexibility based sampling of a water‐dominated interaction scheme , 2004, Protein science : a publication of the Protein Society.
[49] M. Sternberg,et al. Automated prediction of protein function and detection of functional sites from structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[50] A. Edwards,et al. Structural proteomics: a tool for genome annotation. , 2004, Current opinion in chemical biology.
[51] C. Innis,et al. Prediction of functional sites in proteins using conserved functional group analysis. , 2004, Journal of molecular biology.