Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening

Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening

(2023) Yuejiang Yu et al.   Journal of Chemical Theory and Computation

What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?

(2021) Tiziano Tuccinardi   Expert Opinion on Drug Discovery

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

(2021) Mario S. Valdés-Tresanco et al.   Journal of Chemical Theory and Computation

A fast and high-quality charge model for the next generation general AMBER force field

(2020) Xibing He et al.   JOURNAL OF CHEMICAL PHYSICS

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

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

How an alloreactive T-cell receptor achieves peptide and MHC specificity

(2017) Yuan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CaFE: a tool for binding affinity prediction using end-point free energy methods

(2016) Hui Liu et al.   BIOINFORMATICS

Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches

(2016) Govindan Subramanian et al.   Journal of Chemical Information and Modeling

GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning

(2015) C. Paissoni et al.   COMPUTER PHYSICS COMMUNICATIONS

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

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

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

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

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

(2015) Salla I. Virtanen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells

(2013) D. Weiskopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations

(2012) Jun Wang 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 of protein–ligand interactions

(2011) Anita de Ruiter et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration

(2010) Miguel Jorge et al.   Journal of Chemical Theory and Computation

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS