Identification of substrate binding sites in enzymes by computational solvent mapping.

[1]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[2]  R. Jernigan,et al.  Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .

[3]  P. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[4]  G. Petsko,et al.  Crystallography and site-directed mutagenesis of yeast triosephosphate isomerase: what can we learn about catalysis from a "simple" enzyme? , 1987, Cold Spring Harbor symposia on quantitative biology.

[5]  R M Stroud,et al.  The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis. , 1988, Science.

[6]  Brian W. Matthews,et al.  Structural basis of the action of thermolysin and related zinc peptidases , 1988 .

[7]  B. Honig,et al.  Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.

[8]  M Karplus,et al.  Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. , 1990, Science.

[9]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[10]  W. Lipscomb,et al.  Crystal structure of fructose-1,6-bisphosphatase complexed with fructose 6-phosphate, AMP, and magnesium. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Karplus,et al.  Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.

[12]  Crystal structure of the neutral form of fructose 1,6-bisphosphatase complexed with regulatory inhibitor fructose 2,6-bisphosphate at 2.6-A resolution. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Robert E. Bruccoleri,et al.  Grid positioning independence and the reduction of self‐energy in the solution of the Poisson—Boltzmann equation , 1993, J. Comput. Chem..

[14]  W. Saenger,et al.  Computer modeling studies on the binding of 2',5'-linked dinucleoside phosphates to ribonuclease T1-influence of subsite interactions on the substrate specificity. , 1993, Journal of biomolecular structure & dynamics.

[15]  H. Yamada,et al.  Regiochemistry of cytochrome P450 isozymes. , 1994, Annual review of pharmacology and toxicology.

[16]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[17]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[18]  I. Vakser Protein docking for low-resolution structures. , 1995, Protein engineering.

[19]  J M Thornton,et al.  LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. , 1995, Protein engineering.

[20]  V. Villeret,et al.  Crystallographic evidence for the action of potassium, thallium, and lithium ions on fructose-1,6-bisphosphatase. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[21]  W. Rutter,et al.  Structural origins of substrate discrimination in trypsin and chymotrypsin. , 1995, Biochemistry.

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

[23]  G. H. Reed,et al.  Structural and mechanistic studies of enolase. , 1996, Current opinion in structural biology.

[24]  I. S. Ridder,et al.  Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range. , 1996, Biochemistry.

[25]  G. H. Reed,et al.  A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution. , 1996, Biochemistry.

[26]  M. Karplus,et al.  A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .

[27]  D. Ringe,et al.  Locating and characterizing binding sites on proteins , 1996, Nature Biotechnology.

[28]  Karen N. Allen,et al.  An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins , 1996 .

[29]  Daniel A. Gschwend,et al.  Molecular docking towards drug discovery , 1996, Journal of molecular recognition : JMR.

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

[31]  Substrate Docking Algorithms and Prediction of the Substrate Specificity of Cytochrome P450cam and Its L244A Mutant , 1997 .

[32]  J. Steyaert A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions. , 1997, European journal of biochemistry.

[33]  W. Lipscomb,et al.  Recent Advances in Zinc Enzymology , 1997 .

[34]  L Lebioda,et al.  Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution. , 1997, Biochemistry.

[35]  C. DeLisi,et al.  Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.

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

[37]  Evidence by site-directed mutagenesis that arginine 203 of thermolysin and arginine 717 of neprilysin (neutral endopeptidase) play equivalent critical roles in substrate hydrolysis and inhibitor binding. , 1997, Biochemistry.

[38]  G. Otting,et al.  Organic solvents identify specific ligand binding sites on protein surfaces , 1997, Nature Biotechnology.

[39]  J. Brewer,et al.  Significance of the enzymatic properties of yeast S39A enolase to the catalytic mechanism. , 1998, Biochimica et biophysica acta.

[40]  N. Willassen,et al.  The crystal structure of anionic salmon trypsin in complex with bovine pancreatic trypsin inhibitor. , 1998, European journal of biochemistry.

[41]  M. Fournié-Zaluski,et al.  Differences in transition state stabilization between thermolysin (EC 3.4.24.27) and neprilysin (EC 3.4.24.11) , 1998, FEBS letters.

[42]  D. Baker,et al.  Clustering of low-energy conformations near the native structures of small proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  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.

[44]  Herbert Edelsbrunner,et al.  On the Definition and the Construction of Pockets in Macromolecules , 1998, Discret. Appl. Math..

[45]  I. S. Ridder,et al.  Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase. , 1999, Biochemistry.

[46]  Modification of ribonuclease T1 specificity by random mutagenesis of the substrate binding segment. , 1999, Biochemistry.

[47]  I. Vakser,et al.  A systematic study of low-resolution recognition in protein--protein complexes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R E Hubbard,et al.  Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol , 1999, Proteins.

[49]  Role of His159 in yeast enolase catalysis. , 1999, Biochemistry.

[50]  Analysis of the Binding Surfaces of Proteins , 1999 .

[51]  Jacquelyn S. Fetrow,et al.  Structural genomics and its importance for gene function analysis , 2000, Nature Biotechnology.

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

[53]  R. Stevens,et al.  Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. , 2000, Current opinion in structural biology.

[54]  J. Brewer,et al.  The H159A mutant of yeast enolase 1 has significant activity. , 2000, Biochemical and biophysical research communications.

[55]  R. Kazlauskas,et al.  Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. , 2000, Current opinion in chemical biology.

[56]  H. Fromm,et al.  Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes. , 2000, Biochemistry.

[57]  A Sali,et al.  Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Antje Rottmann,et al.  Modeling, mutagenesis, and structural studies on the fully conserved phosphate‐binding loop (Loop 8) of triosephosphate isomerase: Toward a new substrate specificity , 2001, Proteins.

[59]  D E Koshland,et al.  Propagating conformational changes over long (and short) distances in proteins , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Probing functional perfection in substructures of ribonuclease T1: double combinatorial random mutagenesis involving Asn43, Asn44, and Glu46 in the guanine binding loop. , 2001, Biochemistry.

[61]  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.

[62]  R E Hubbard,et al.  Experimental and computational mapping of the binding surface of a crystalline protein. , 2001, Protein engineering.

[63]  Sandor Vajda,et al.  Computational mapping identifies the binding sites of organic solvents on proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Marek Wojciechowski,et al.  Docking of small ligands to low‐resolution and theoretically predicted receptor structures , 2002, J. Comput. Chem..

[65]  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.

[66]  A. Valencia,et al.  Automatic methods for predicting functionally important residues. , 2003, Journal of molecular biology.

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

[68]  Sandor Vajda,et al.  Algorithms for computational solvent mapping of proteins , 2003, Proteins.

[69]  Sandor Vajda,et al.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..