An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Advances in the calculation of binding free energies

(2020) Anita de Ruiter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19

(2020) Rommie E. Amaro et al.   Journal of Chemical Information and Modeling

Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding

(2020) Negin Forouzesh et al.   Journal of Chemical Theory and Computation

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

Mutations Strengthened SARS-CoV-2 Infectivity

(2020) Jiahui Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

(2020) Carolina Corrêa Giron et al.   VIRUS RESEARCH

The coronavirus is mutating — does it matter?

(2020) Ewen Callaway   NATURE

Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein

(2020) Rodrigo A. Moreira et al.   Materials

Effect of nelfinavir stereoisomers on coronavirus main protease: Molecular docking, molecular dynamics simulation and MM/GBSA study

(2020) Mohsen Sargolzaei   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Generalized Born Implicit Solvent Models for Biomolecules

(2019) Alexey V. Onufriev et al.   Annual Review of Biophysics

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4

(2019) Junjie Zou et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Artificial Intelligence for Clinical Trial Design

(2019) Stefan Harrer et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors

(2019) Sukanya Sasmal et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computational prediction of protein–protein binding affinities

(2019) Till Siebenmorgen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach

(2019) Matías Martínez et al.   Journal of Chemical Information and Modeling

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

(2018) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

(2018) Saeed Izadi et al.   Journal of Chemical Theory and Computation

Generalization of the elastic network model for the study of large conformational changes in biomolecules

(2018) Adolfo B. Poma et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods

(2018) Zhe Wang et al.   BIOINFORMATICS

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations

(2017) Ido Y. Ben-Shalom et al.   Journal of Chemical Information and Modeling

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

(2017) Negin Forouzesh et al.   Journal of Chemical Information and Modeling

Water models for biomolecular simulations

(2017) Alexey V. Onufriev et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies ofF. tularensisenoyl-ACP reductase (FabI)

(2015) Pin-Chih Su et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions

(2014) Alexey V. Onufriev et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

(2012) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Efficient Computation of the Total Solvation Energy of Small Molecules via the R6 Generalized Born Model

(2012) Boris Aguilar et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

SwissDock, a protein-small molecule docking web service based on EADock DSS

(2011) A. Grosdidier et al.   NUCLEIC ACIDS RESEARCH

Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii

(2010) Boris Aguilar et al.   Journal of Chemical Theory and Computation

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Consistent van der Waals Radii for the Whole Main Group

(2009) Manjeera Mantina et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH