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Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cncr.23355openalex-snapshot
Molecular basis explanation for imatinib resistance of BCR‐ABL due to T315I and P‐loop mutations from molecular dynamics simulations
inferredcites →https://doi.org/10.1002/jcc.20065openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20587openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
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A molecular mechanics model for imatinib and imatinib:kinase binding
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
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Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl‐transferase P‐site using molecular dynamics simulations with restraining potentials
inferredcites →https://doi.org/10.1002/prot.340040208openalex-snapshot
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
inferredcites →https://doi.org/10.1007/s00214-002-0421-3openalex-snapshot
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase
inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
inferredcites →https://doi.org/10.1016/j.cell.2006.12.038openalex-snapshot
Histone Methylation-Dependent Mechanisms Impose Ligand Dependency for Gene Activation by Nuclear Receptors
inferredcites →https://doi.org/10.1016/j.chembiol.2008.09.007openalex-snapshot
Small Molecule Recognition of c-Src via the Imatinib-Binding Conformation
inferredcites →https://doi.org/10.1016/j.str.2007.01.015openalex-snapshot
c-Src Binds to the Cancer Drug Imatinib with an Inactive Abl/c-Kit Conformation and a Distributed Thermodynamic Penalty
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Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study
inferredcites →https://doi.org/10.1016/s0006-3495(97)78756-3openalex-snapshot
The statistical-thermodynamic basis for computation of binding affinities: a critical review
inferredcites →https://doi.org/10.1016/s0010-4655(00)00215-0openalex-snapshot
Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
inferredcites →https://doi.org/10.1021/ci200153copenalex-snapshot
Understanding the Impact of the P-loop Conformation on Kinase Selectivity
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Predicting Kinase Selectivity Profiles Using Free-Wilson QSAR Analysis
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Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
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Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics
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Improved Treatment of the Protein Backbone in Empirical Force Fields
inferredcites →https://doi.org/10.1021/ja210751topenalex-snapshot
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation
inferredcites →https://doi.org/10.1021/ja405939xopenalex-snapshot
Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases
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Acid−Base Profiling of Imatinib (Gleevec) and Its Fragments
inferredcites →https://doi.org/10.1021/jm0608107openalex-snapshot
Molecular Recognition of Protein Kinase Binding Pockets for Design of Potent and Selective Kinase Inhibitors
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Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome
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Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1021/pr100662sopenalex-snapshot
Protein Kinase−Inhibitor Database: Structural Variability of and Inhibitor Interactions with the Protein Kinase P-Loop
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Comparison of simple potential functions for simulating liquid water
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1073/pnas.0409005102openalex-snapshot
Calculation of absolute protein–ligand binding free energy from computer simulations
inferredcites →https://doi.org/10.1073/pnas.1214330110openalex-snapshot
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
inferredcites →https://doi.org/10.1074/jbc.m110.109660openalex-snapshot
Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
inferredcites →https://doi.org/10.1107/s0907444906047287openalex-snapshot
Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia
inferredcites →https://doi.org/10.1126/science.1095920openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.289.5486.1938openalex-snapshot
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inferredcites →https://doi.org/10.1158/0008-5472.can-08-3953openalex-snapshot
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inferredcites →https://doi.org/10.1158/1078-0432.ccr-09-1068openalex-snapshot
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inferredcites →https://doi.org/10.1172/jci9083openalex-snapshot
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inferredcites →https://doi.org/10.1182/blood-2004-08-3097openalex-snapshot
The development of imatinib as a therapeutic agent for chronic myeloid leukemia
inferredcites →https://doi.org/10.1529/biophysj.106.084301openalex-snapshot
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inferredcites →https://doi.org/10.2174/157489209788452867openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.25715openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.25401openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.25611openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-015-9841-8openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbapap.2015.03.014openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bpj.2025.04.020openalex-snapshot
Path sampling challenges in large biomolecular systems: RETIS and REPPTIS for ABL-imatinib kinetics
inferred← citeshttps://doi.org/10.1016/j.chemolab.2015.10.013openalex-snapshot
Computational study on the inhibition mechanism of a cyclic peptide MaD5 to PfMATE: Insight from molecular dynamics simulation, free energy calculation and dynamical network analysis
inferred← citeshttps://doi.org/10.1016/j.comptc.2024.114675openalex-snapshot
The study on the electron transfer between cytochrome c and single-walled carbon nanotube – The calculations of the reorganization free energy, the coupling matrix element and the rate constant
inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.117369openalex-snapshot
Advancing Src kinase inhibition: From structural design to therapeutic innovation - A comprehensive review
inferred← citeshttps://doi.org/10.1016/j.semcancer.2020.04.007openalex-snapshot
Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs
inferred← citeshttps://doi.org/10.1021/acs.accounts.7b00012openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c00534openalex-snapshot
Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00815openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00897openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.4c02313openalex-snapshot
Predicting Resistance to Small Molecule Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00240openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00452openalex-snapshot
Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein–Ligand to RNA-Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00398openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01823openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00564openalex-snapshot
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00739openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01389openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00738openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c00264openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c04100openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c01412openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b09406openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jacs.6b11467openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jacs.7b08938openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jm501603hopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jp511792aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c5mb00246jopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c7cp03443aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c8cp01524dopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c8ob01526kopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/d1cp00266jopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/d2cp03080bopenalex-snapshot
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inferred← citeshttps://doi.org/10.1042/bcj20170299openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/00268976.2024.2374465openalex-snapshot
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inferred← citeshttps://doi.org/10.1134/s1068162020020089openalex-snapshot
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inferred← citeshttps://doi.org/10.1140/epjb/s10051-021-00207-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0130203openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0132221openalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-zpp2jopenalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv.13132814openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fmolb.2015.00027openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fmolb.2020.00136openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms24032649openalex-snapshot
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inferred← citeshttps://doi.org/10.37349/eds.2025.1008109openalex-snapshot
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inferred← citeshttps://doi.org/10.7554/elife.83368openalex-snapshot
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