Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2023-06-17
DOI
10.1093/bib/bbad218
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now