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Journal of Molecular Biology, ISSN 0022-2836, 04/2017, Volume 429, Issue 7, pp. 930 - 947
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 01/2004, Volume 25, Issue 1, pp. 28 - 40
A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational... 
alchemical transformation | free energy simulation | perturbation calculation | overlap sampling | Alchemical transformation | Overlap sampling | Free energy simulation | Perturbation calculation | ERRORS | PHASE-SPACE | POTENTIAL FUNCTIONS | CHEMISTRY, MULTIDISCIPLINARY | ACCURACY | MOLECULAR SIMULATION | FLUID | DYNAMICS | SYSTEMS | COMPUTATION | WATER
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 03/2019, Volume 150, Issue 12
Journal Article
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2017, Volume 13, Issue 5, pp. 1924 - 1933
The present paper is intended to be a comprehensive assessment and rationalization, from a statistical mechanics perspective, of existing alchemical theories... 
FREE-ENERGY CALCULATIONS | MUTANT | FORCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | COMPUTATION | POTENTIALS | MOLECULAR-DYNAMICS SIMULATIONS | T4 LYSOZYME | AFFINITIES | PREDICTION
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 1/2013, Volume 110, Issue 5, pp. 1664 - 1669
Tyrosine kinases present attractive drug targets for specific types of cancers. Gleevec, a well-known therapeutic agent against chronic myelogenous leukemia,... 
Molecules | Thermodynamics | Solvents | Roux | Molecular dynamics | Atoms | Ligands | Chronic myeloid leukemia | Electrostatics | Free energy | Sampling | Alchemical free energy perturbation | CHRONIC MYELOGENOUS LEUKEMIA | BINDING FREE-ENERGY | TYROSINE KINASE | MULTIDISCIPLINARY SCIENCES | sampling | BCR-ABL | thermodynamics | alchemical free energy perturbation | HISTOGRAM ANALYSIS METHOD | CHRONIC MYELOID-LEUKEMIA | INACTIVE CONFORMATION | RESTRAINING POTENTIALS | MOLECULAR-DYNAMICS SIMULATIONS | C-SRC | Proto-Oncogene Proteins c-abl - antagonists & inhibitors | Humans | Leukemia, Myelogenous, Chronic, BCR-ABL Positive - drug therapy | Crystallography, X-Ray | Piperazines - metabolism | Proto-Oncogene Proteins pp60(c-src) - chemistry | Pyrimidines - metabolism | Binding Sites | Binding, Competitive | Leukemia, Myelogenous, Chronic, BCR-ABL Positive - enzymology | Protein Structure, Tertiary | Proto-Oncogene Proteins c-abl - chemistry | Models, Molecular | Proto-Oncogene Proteins pp60(c-src) - antagonists & inhibitors | Pyrimidines - pharmacology | Imatinib Mesylate | Piperazines - pharmacology | Proto-Oncogene Proteins pp60(c-src) - metabolism | Protein Binding | Proto-Oncogene Proteins c-abl - metabolism | Protein Conformation | Protein Kinase Inhibitors - pharmacology | Benzamides | Protein Kinase Inhibitors - metabolism | Tyrosine | Physiological aspects | Research | Phosphotransferases | Health aspects | Protein binding | Biological Sciences | Physical Sciences
Journal Article
06/2017, ISBN 9780128032015, Volume 3-8
Over the past decade, the accuracy of free energy methods and their usefulness in computer-aided drug design have greatly benefited from a number of technical... 
Collective variables | Binding kinetics | Free energy perturbation | Drug binding | Cryptic pockets | Alchemical methods | Thermodynamic integration | Metadynamics | Conformational changes | Free energy
Book Chapter
Journal of Computational Chemistry, ISSN 0192-8651, 05/2011, Volume 32, Issue 7, pp. 1303 - 1319
Journal Article
Physical chemistry chemical physics : PCCP, ISSN 1463-9076, 07/2019, Volume 21, Issue 25, pp. 13826 - 13834
Free energy perturbation (FEP) approaches with stratification have seen widespread and increasing use in computational studies of biologically relevant... 
Thermodynamics | Protein Kinase Inhibitors - chemistry | Uncertainty | Solvents - chemistry | Molecular Conformation | Water - chemistry | Models, Molecular | Quinazolines - chemistry | Octanols - chemistry
Journal Article