Connectivity and binding‐site recognition: Applications relevant to drug design
暂无分享,去创建一个
Christopher J. R. Illingworth | Paul D. Scott | Matthew P. Campbell | Kevin E. B. Parkes | Christopher R. Snell | Christopher A. Reynolds | Matthew P. Campbell | P. Scott | C. Reynolds | C. Snell | M. Campbell | K. Parkes | C. Illingworth | C. Reynolds
[1] M. Karplus,et al. Transition state contact orders correlate with protein folding rates. , 2005, Journal of molecular biology.
[2] C. Ptak,et al. Probing the allosteric modulator binding site of GluR2 with thiazide derivatives. , 2009, Biochemistry.
[3] C. Venkatachalam,et al. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.
[4] Marta Filizola,et al. Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method. , 2002, Protein engineering.
[5] Sophie Sacquin-Mora,et al. Investigating the local flexibility of functional residues in hemoproteins. , 2006, Biophysical journal.
[6] John Ellis,et al. Mutational Disruption of a Conserved Disulfide Bond in Muscarinic Acetylcholine Receptors Attenuates Positive Homotropic Cooperativity between Multiple Allosteric Sites and Has Subtype-Dependent Effects on the Affinities of Muscarinic Allosteric Ligands , 2007, Molecular Pharmacology.
[7] Takashi Yonetani,et al. Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-A resolution. A novel allosteric binding site in R-state hemoglobin. , 2002 .
[8] Sophie Sacquin-Mora,et al. Locating the active sites of enzymes using mechanical properties , 2007, Proteins.
[9] U. Hobohm,et al. Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.
[10] Olivier Lichtarge,et al. Prediction and confirmation of a site critical for effector regulation of RGS domain activity , 2001, Nature Structural Biology.
[11] M. Eriksson,et al. Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding. , 1997, Structure.
[12] Leif A. Eriksson,et al. Theoretical Biochemistry: Processes and Properties of Biological Systems , 2001 .
[13] Michelle R. Arkin,et al. Binding of small molecules to an adaptive protein–protein interface , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[14] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[15] A. Hamilton,et al. Strategies for targeting protein-protein interactions with synthetic agents. , 2005, Angewandte Chemie.
[16] Paul D. Scott,et al. Dimerization of G-protein-coupled receptors. , 2001 .
[17] David C Fry,et al. Protein-protein interactions as targets for small molecule drug discovery. , 2006, Biopolymers.
[18] Georgios G. Gkoutos,et al. Lipid-facing correlated mutations and dimerization in G-protein coupled receptors. , 2001, Protein engineering.
[19] J. MacQueen. Some methods for classification and analysis of multivariate observations , 1967 .
[20] A. Elcock,et al. Identification of protein oligomerization states by analysis of interface conservation , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[21] Celerino Abad-Zapatero,et al. Benzoxazole benzenesulfonamides are novel allosteric inhibitors of fructose-1,6-bisphosphatase with a distinct binding mode. , 2006, Bioorganic & medicinal chemistry letters.
[22] Christopher L. McClendon,et al. Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.
[23] Richard M. Jackson,et al. Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces , 2006, Bioinform..
[24] Richard M. Jackson,et al. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..
[25] Paul D. Scott,et al. Entropy and oligomerization in GPCRs , 2007, Journal of Molecular Neuroscience.
[26] E. Shakhnovich,et al. Topological determinants of protein folding , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[27] F E Cohen,et al. Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[28] J. Wells,et al. Discovery of an allosteric site in the caspases. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[29] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[30] Bruck Taddese,et al. Bioinformatics and molecular modelling approaches to GPCR oligomerization. , 2010, Current opinion in pharmacology.
[31] M Karplus,et al. Small-world view of the amino acids that play a key role in protein folding. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[32] J Andrew McCammon,et al. Discovery of a novel binding trench in HIV integrase. , 2004, Journal of medicinal chemistry.
[33] Christopher A. Reynolds,et al. Chapter 9 - Modelling G-protein coupled receptors , 2001 .
[34] Ashish V. Tendulkar,et al. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. , 2003, Journal of molecular biology.
[35] M Hendlich,et al. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.
[36] Michel Bouvier,et al. Functional rescue of the constitutively internalized V2 vasopressin receptor mutant R137H by the pharmacological chaperone action of SR49059. , 2004, Molecular endocrinology.
[37] P. Goodford. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.
[38] M. J. Newman,et al. Inhibition of Fructose-1,6-bisphosphatase by a New Class of Allosteric Effectors* , 2003, Journal of Biological Chemistry.
[39] Tsutomu Kouyama,et al. Crystal structure of squid rhodopsin , 2008, Nature.
[40] Neil D. Rawlings,et al. MEROPS: the peptidase database , 2009, Nucleic Acids Res..
[41] Manfred Burghammer,et al. Structure of bovine rhodopsin in a trigonal crystal form. , 2003, Journal of molecular biology.
[42] Gil Amitai,et al. Network analysis of protein structures identifies functional residues. , 2004, Journal of molecular biology.
[43] D Eisenberg,et al. The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition. , 2001, Biochemistry.
[44] David S. Goodsell,et al. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 , 1996, J. Comput. Aided Mol. Des..
[45] Gail J. Bartlett,et al. Analysis of catalytic residues in enzyme active sites. , 2002, Journal of molecular biology.
[46] Judith Klein-Seetharaman,et al. Additive Effects of Chlorin E6 and Metal Ion Binding on the Thermal Stability of Rhodopsin In Vitro † , 2009, Photochemistry and photobiology.
[47] M. Karplus,et al. Three key residues form a critical contact network in a protein folding transition state , 2001, Nature.
[48] G. Alton,et al. Characterization of the CHK1 allosteric inhibitor binding site. , 2009, Biochemistry.
[49] Liang Tong,et al. Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate. , 2002, Structure.
[50] M R Harris,et al. PLIM: A protein–ligand interaction modeller , 1993, Journal of molecular recognition : JMR.
[51] W. Richards,et al. Identification of ligand binding sites on proteins using a multi-scale approach. , 2002, Journal of the American Chemical Society.
[52] 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..
[53] J. Thornton,et al. PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.
[54] Arthur Christopoulos,et al. Allosteric modulation of G protein-coupled receptors. , 2007, Annual review of pharmacology and toxicology.
[55] Christopher J. R. Illingworth,et al. Computational studies of Family A and Family B GPCRs. , 2007, Biochemical Society transactions.
[56] R. Horuk,et al. I want a new drug: G-protein-coupled receptors in drug development. , 2006, Drug discovery today.
[57] K Ulrich Wendt,et al. Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors. , 2008, Biochemistry.
[58] J. Klein-Seetharaman,et al. Single-cysteine substitution mutants at amino acid positions 55-75, the sequence connecting the cytoplasmic ends of helices I and II in rhodopsin: reactivity of the sulfhydryl groups and their derivatives identifies a tertiary structure that changes upon light-activation. , 1999, Biochemistry.
[59] U. Hobohm,et al. Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.
[60] Jaime Prilusky,et al. Automated analysis of interatomic contacts in proteins , 1999, Bioinform..
[61] Robert P Bywater,et al. Recognition of privileged structures by G-protein coupled receptors. , 2004, Journal of medicinal chemistry.
[62] J. Kew,et al. Mutational Analysis and Molecular Modeling of the Allosteric Binding Site of a Novel, Selective, Noncompetitive Antagonist of the Metabotropic Glutamate 1 Receptor* , 2003, The Journal of Biological Chemistry.
[63] A. A. Jensen,et al. Structure, pharmacology and therapeutic prospects of family C G-protein coupled receptors. , 2007, Current drug targets.
[64] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[65] D. Hirschberg,et al. Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. , 2009, Nature chemical biology.
[66] D. Fairlie,et al. Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. , 2000, Journal of medicinal chemistry.