Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges-Reference-Cited by-同舟云学术

Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

Published:2021-05-24 Issue:6 Volume:35 Page:721-729
ISSN:0920-654X
Container-title:Journal of Computer-Aided Molecular Design
language:en
Short-container-title:J Comput Aided Mol Des

Author:

Casbarra Lorenzo,Procacci Piero^ORCID

Abstract

AbstractWe systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

Funder

Università degli Studi di Firenze

Publisher

Springer Science and Business Media LLC

Subject

Physical and Theoretical Chemistry,Computer Science Applications,Drug Discovery

Link

https://link.springer.com/content/pdf/10.1007/s10822-021-00388-4.pdf

Reference42 articles.

1. Muddana Hari S, Varnado C. Daniel, Bielawski Christopher W, Urbach Adam R, Isaacs Lyle, Geballe Matthew T, Gilson Michael K (2012) Blind prediction of host-guest binding affinities: a new sampl3 challenge. J Comput Aided Mol Des 26(5):475–487

2. Muddana Hari S, Fenley Andrew T, Mobley David L, Gilson Michael K (2014) The sampl4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des 28(4):305–317

3. Yin Jian, Henriksen Niel M, Slochower David R, Shirts Michael R, Chiu Michael W, Mobley David L, Gilson Michael K (2016) Overview of the sampl5 host–guest challenge: Are we doing better? J Comput Aided Mol Des 31:1–19