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

Casbarra, Lorenzo; Procacci, Piero

Casbarra, Lorenzo; Procacci, Piero.

Casbarra L; University of Florence, Department of Chemistry, Via Lastruccia n. 3, I-50019, Sesto Fiorentino, FI, Italy.
Procacci P; University of Florence, Department of Chemistry, Via Lastruccia n. 3, I-50019, Sesto Fiorentino, FI, Italy. procacci@unifi.it.

J Comput Aided Mol Des ; 35(6): 721-729, 2021 06.

Article in English | MEDLINE | ID: covidwho-1549468

ABSTRACT

ABSTRACT

We 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.

Subject(s)

Proteins/chemistry; Ligands; Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; Reproducibility of Results; Retrospective Studies; Software; Solvents/chemistry; Thermodynamics

Keywords

Binding free energy; Crooks theorem; Fast switching; HREX; Hamiltonian replica exchange; Non-equilibrium; SAMPL7; Solute tempering; Torsional tempering

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Proteins Type of study: Observational study / Prognostic study Language: English Journal: J Comput Aided Mol Des Journal subject: Molecular Biology / Biomedical Engineering Year: 2021 Document Type: Article Affiliation country: S10822-021-00388-4

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