ArticleJournal of biological physics2011
Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor.
Article in Journal of biological physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 33 citations in OpenAlex.
- Simulating protein-ligand binding with neural network potentials.Chemical science · 2020Article
- Molecular docking and ADMET analysis of hydroxamic acids as HDAC2 inhibitors.Bioinformation · 2019Article
- Combined UMC- DFT prediction of electron-hole coupling in unit cells of pentacene crystals.Journal of molecular modeling · 2017Article
- Insight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KIT.PloS one · 2016Article
- Conformational landscape and low lying excited states of imatinib.Journal of molecular modeling · 2015Article
- Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases.Journal of the American Chemical Society · 2013Article
- Explaining why Gleevec is a specific and potent inhibitor of Abl kinase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.Journal of chemical theory and computation · 2012Article
- Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex.Journal of molecular modeling · 2012Article
- Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study.Journal of computer-aided molecular design · 2012Article
- Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses.Journal of computer-aided molecular design · 2011Article
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Authors and funding
2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
We report a Quantum mechanics/Molecular Mechanics-Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib.Electronic supplementary material The online version of this article (doi:10.1007/s10867-010-9199-z) contains supplementary material, which is available to authorized users.
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