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
Chemical Physics Letters – Elsevier
Published: Mar 1, 2018
It’s your single place to instantly
discover and read the research
that matters to you.
Enjoy affordable access to
over 12 million articles from more than
10,000 peer-reviewed journals.
All for just $49/month
Read as many articles as you need. Full articles with original layout, charts and figures. Read online, from anywhere.
Keep up with your field with Personalized Recommendations and Follow Journals to get automatic updates.
It’s easy to organize your research with our built-in tools.
Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.
All the latest content is available, no embargo periods.
“Hi guys, I cannot tell you how much I love this resource. Incredible. I really believe you've hit the nail on the head with this site in regards to solving the research-purchase issue.”Daniel C.
“Whoa! It’s like Spotify but for academic articles.”@Phil_Robichaud
“I must say, @deepdyve is a fabulous solution to the independent researcher's problem of #access to #information.”@deepthiw
“My last article couldn't be possible without the platform @deepdyve that makes journal papers cheaper.”@JoseServera