Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular... Chemical Physics Letters 695 (2018) 69–78 Contents lists available at ScienceDirect Chemical Physics Letters journal homepage: www.elsevier.com/locate/cplett Research paper Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test Preeti Pandey, Rakesh Srivastava, Pradipta Bandyopadhyay School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India article i nfo abstract Article history: The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of Received 29 October 2017 protein–ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, In final form 30 January 2018 Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. Available online 1 February 2018 None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qual- itatively different result for the polar part of solvation. 2018 Elsevier B.V. All rights reserved. 1. Introduction Hence, there is a continuous http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Chemical Physics Letters Elsevier

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

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Publisher
Elsevier
Copyright
Copyright © 2018 Elsevier B.V.
ISSN
0009-2614
eISSN
1873-4448
D.O.I.
10.1016/j.cplett.2018.01.059
Publisher site
See Article on Publisher Site

Abstract

Chemical Physics Letters 695 (2018) 69–78 Contents lists available at ScienceDirect Chemical Physics Letters journal homepage: www.elsevier.com/locate/cplett Research paper Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test Preeti Pandey, Rakesh Srivastava, Pradipta Bandyopadhyay School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India article i nfo abstract Article history: The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of Received 29 October 2017 protein–ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, In final form 30 January 2018 Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. Available online 1 February 2018 None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qual- itatively different result for the polar part of solvation. 2018 Elsevier B.V. All rights reserved. 1. Introduction Hence, there is a continuous

Journal

Chemical Physics LettersElsevier

Published: Mar 1, 2018

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