Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity

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Computational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/JA504146X
P932PMC publication ID4210138
P698PubMed publication ID25243930
P5875ResearchGate publication ID266028238

P2093author name stringBenoît Roux
Lei Huang
Yen-Lin Lin
Yilin Meng
P2860cites workLessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemiaQ24599829
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Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase ConformationsQ27654059
All-atom empirical potential for molecular modeling and dynamics studies of proteinsQ27860468
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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulationsQ29547631
Predicting kinase selectivity profiles using Free-Wilson QSAR analysisQ33362111
Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinasesQ33631185
Calculation of absolute protein-ligand binding free energy from computer simulationsQ33784404
The statistical-thermodynamic basis for computation of binding affinities: a critical reviewQ33915676
Inhibition of the Abl protein-tyrosine kinase in vitro and in vivo by a 2-phenylaminopyrimidine derivative.Q34370094
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentialsQ35051978
Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).Q35169470
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy CalculationsQ35169555
Protein Kinase−Inhibitor Database: Structural Variability of and Inhibitor Interactions with the Protein Kinase P-LoopQ35606325
Protein kinase inhibitors: insights into drug design from structure.Q35697409
The development of imatinib as a therapeutic agent for chronic myeloid leukemiaQ35993288
Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptorsQ36014589
Explaining why Gleevec is a specific and potent inhibitor of Abl kinaseQ36582978
Molecular recognition of protein kinase binding pockets for design of potent and selective kinase inhibitorsQ36723753
Computations of standard binding free energies with molecular dynamics simulationsQ37335295
Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinasesQ40188101
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation studyQ42536182
Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosomeQ42978880
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentialsQ43164251
A molecular mechanics model for imatinib and imatinib:kinase bindingQ43216200
Attacking cancer at its foundationQ43265336
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulationsQ44694277
Improved treatment of the protein backbone in empirical force fields.Q44735024
Acid-base profiling of imatinib (gleevec) and its fragments.Q45212838
Basis for resistance to imatinib in 16 BCR-ABL mutants as determined using molecular dynamics.Q45972946
Molecular basis explanation for imatinib resistance of BCR-ABL due to T315I and P-loop mutations from molecular dynamics simulationsQ46703844
Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A Mutant.Q53190267
Understanding the impact of the P-loop conformation on kinase selectivity.Q54590322
Mechanisms of Resistance to Imatinib and Second-Generation Tyrosine Inhibitors in Chronic Myeloid Leukemia.Q54703960
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparisonQ57000556
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive ConformationQ58465773
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculationsQ79864597
P433issue42
P407language of work or nameEnglishQ1860
P304page(s)14753-14762
P577publication date2014-10-07
P1433published inJournal of the American Chemical SocietyQ898902
P1476titleComputational study of Gleevec and G6G reveals molecular determinants of kinase inhibitor selectivity
P478volume136

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cites work (P2860)
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Q45934140Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
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Q35493874Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors.
Q38998249Evolution and intelligent design in drug development
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Q47662738Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity.
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Q28546110Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity

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