Výsledky vyhledávání - "Djamal Bouzida"

Structural modifications of a 3-methoxy-2-aminopyridine compound to reduce potential for mutagenicity and time-dependent drug–drug interaction

Autor: Kephart Susan Elizabeth, Annette John-Baptiste, Deal Judith G, Danlin Gu, Shubha Bagrodia, Cui Jingrong Jean, Shinji Yamazaki, Djamal Bouzida, Pairish Mason Alan, Evan Smith, Chuangxing Guo, Robert Steven Kania, Dong Liming, Angelica Linton, Indrawan James Mcalpine, Cynthia Louise Palmer

Publikováno v: Bioorganic & Medicinal Chemistry Letters. 22:7605-7609

( S )-1-((4-(3-(6-Amino-5-methoxypyridin-3-yl)-1-isopropyl-1 H -pyrazol-4-yl)pyrimidin-2-yl)amino)propan-2-ol, 1 , was recently identified as a potent inhibitor of the oncogenic kinase bRAF. Compounds containing 3-methoxy-2-aminopyridine, as in 1 , c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac6f7691c31b4bb441f40edfbab8cb91
https://doi.org/10.1016/j.bmcl.2012.10.011

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Identification of novel pyrrolopyrazoles as protein kinase C β II inhibitors

Autor: Seiji Nukui, Chunfeng Yin, Jennifer Lafontaine, Djamal Bouzida, Botrous Iriny, Jordan R. Jensen, Stephanie Scales, Eileen Valenzuela Tompkins, Ru Zhou, Sarah Johnson, Mingying He, Jihong Lou, Gordon Alton, Yufeng Hong, Hui Li, Stephan Grant

Publikováno v: Bioorganic & Medicinal Chemistry Letters. 21:584-587

A novel series of pyrrolopyrazole-based protein kinase C β II inhibitors has been identified from high-throughput screening. Herein, we report our initial structure-activity relationship studies with a focus on optimizing compound ligand efficiency

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e7d7b09b217c6fb2ed7457aef0b5f941
https://doi.org/10.1016/j.bmcl.2010.10.032

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Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: The energy landscape analysis of a hot spot at the intermolecular interface

Autor: Gennady M. Verkhivker, Djamal Bouzida, Peter W. Rose, Paul A. Rejto, Daniel K. Gehlhaar, Stephan T. Freer

Publikováno v: Proteins: Structure, Function, and Genetics. 48:539-557

Monte Carlo simulations of molecular recognition at the consensus binding site of the constant fragment (Fc) of human immunoglobulin G (Ig) protein have been performed to analyze structural and thermodynamic aspects of binding for the 13-residue cycl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d82c9c2f3b471b1cdbadacb2b9b3fc14
https://doi.org/10.1002/prot.10164

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Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides

Autor: Tami Marrone, Daniel K. Gehlhaar, Stephan T. Freer, Djamal Bouzida, Paul A. Rejto, Anthony B. Colson, Sandra Arthurs, Brock A. Luty, Lana Schaffer, Veda Larson, Peter W. Rose, Gennady M. Verkhivker

Publikováno v: Journal of Medicinal Chemistry. 45:72-89

Structure and energetics of the Src Src Homology 2 (SH2) domain binding with the recognition phosphopeptide pYEEI and its mutants are studied by a hierarchical computational approach. The proposed structure prediction strategy includes equilibrium sa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a57cc6ee9d43f15ec8167d0753c62fbe
https://doi.org/10.1021/jm0101141

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Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

Autor: Daniel K. Gehlhaar, Stephan T. Freer, Tami Marrone, Veda Larson, Peter W. Rose, Anthony B. Colson, Djamal Bouzida, Gennady M. Verkhivker, Brock A. Luty, Sandra Arthurs, Paul A. Rejto

Publikováno v: Chemical Physics Letters. 336:495-503

Thermodynamic and kinetic aspects of ligand–protein binding are studied for the methotrexate–dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the nati

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::7d53f594d7bab1374de6deb26730a4ed
https://doi.org/10.1016/s0009-2614(01)00161-0

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[Untitled]

Autor: Brock A. Luty, Peter W. Rose, Tami Marrone, Anthony B. Colson, Veda Larson, Sandra Arthurs, Djamal Bouzida, Daniel K. Gehlhaar, Stephan T. Freer, Paul A. Rejto, Gennady M. Verkhivker

Publikováno v: Journal of Computer-Aided Molecular Design. 14:731-751

Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligand-protein systems by a combined thermodynamic and kinetic analysis of the binding energy landscapes. Misdocked predictions in ligand-protein

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d915ab663d1b699766569a40103434d4
https://doi.org/10.1023/a:1008158231558

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Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions

Autor: Veda Larson, Sandra Arthurs, Gennady M. Verkhivker, Djamal Bouzida, Anthony B. Colson, Daniel K. Gehlhaar, Stephan T. Freer, Brock A. Luty, Peter W. Rose, Paul A. Rejto, Tami Marrone

Publikováno v: Journal of Molecular Recognition. 12:371-389

The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)-dihydrofolate reductase (DHFR) ligand-protein system are investigated by the binding energy landscape approach. The impact of 'hot' and 'cold' errors in ligand

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d5340b1174ac04a48bc1180213712c5b
https://doi.org/10.1002/(sici)1099-1352(199911/12)12:6<371::aid-jmr479>3.0.co

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Examining ligand-protein interactions with binding-energy landscapes

Autor: Djamal Bouzida, Gennady M. Verkhivker, Paul A. Rejto

Publikováno v: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 101:138-142

Binding-energy landscapes are used to investigate the thermodynamics of molecular recognition for the pteridine ring, a recognition anchor in binding with dihydrofolate reductase, and two molecules with the same shape but different heteroatom substit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::39b7912026861db224c267127dade794
https://doi.org/10.1007/s002140050420

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Multidimensional free-energy calculations using the weighted histogram analysis method

Autor: Robert H. Swendsen, Peter A. Kollman, John M. Rosenberg, Shankar Kumar, Djamal Bouzida

Publikováno v: Journal of Computational Chemistry. 16:1339-1350

The recently formulated weighted histogram analysis method (WHAM)1 is an extension of Ferrenberg and Swendsen's multiple histogram technique for free-energy and potential of mean force calculations. As an illustration of the method, we have calculate

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::92dcc208ad80f62d8bd7590740c1a138
https://doi.org/10.1002/jcc.540161104

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