Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset
Authors
Keywords
-
Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 34, Issue 11, Pages 1133-1145
Publisher
Springer Science and Business Media LLC
Online
2020-08-27
DOI
10.1007/s10822-020-00339-5
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures
- (2019) Mei Qian Yau et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
- (2019) Léa El Khoury et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment
- (2018) Jason S.E. Loo et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs?
- (2018) Krishna Sriram et al. MOLECULAR PHARMACOLOGY
- Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?
- (2018) David Ramírez et al. MOLECULES
- Comparative Assessment of Scoring Functions: The CASF-2016 Update
- (2018) Minyi Su et al. Journal of Chemical Information and Modeling
- GPCRdb in 2018: adding GPCR structure models and ligands
- (2017) Gáspár Pándy-Szekeres et al. NUCLEIC ACIDS RESEARCH
- GPCR-Bench: A Benchmarking Set and Practitioners’ Guide for G Protein-Coupled Receptor Docking
- (2016) Dahlia R. Weiss et al. Journal of Chemical Information and Modeling
- Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis
- (2016) Changhao Wang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
- (2016) Zhe Wang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening
- (2015) Salla I. Virtanen et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Methodological advances: the unsung heroes of the GPCR structural revolution
- (2015) Eshan Ghosh et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- 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
- Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure
- (2013) Andrew Anighoro et al. Journal of Chemical Information and Modeling
- Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties
- (2013) Christian L. Wennberg et al. Journal of Chemical Theory and Computation
- Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations
- (2012) Miriam Sgobba et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines
- (2012) Thijs Beuming et al. Journal of Chemical Information and Modeling
- MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement
- (2012) Paulette A. Greenidge et al. Journal of Chemical Information and Modeling
- Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease
- (2012) Daniel P. Oehme et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
- (2012) Michael M. Mysinger et al. JOURNAL OF MEDICINAL CHEMISTRY
- Structure-based drug screening for G-protein-coupled receptors
- (2012) Brian K. Shoichet et al. TRENDS IN PHARMACOLOGICAL SCIENCES
- Progress in Structure Based Drug Design for G Protein-Coupled Receptors
- (2011) Miles Congreve et al. JOURNAL OF MEDICINAL CHEMISTRY
- Virtual screening using molecular simulations
- (2011) Tianyi Yang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
- (2010) Tingjun Hou et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions
- (2010) Nidhi Singh et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening
- (2009) Giulio Rastelli et al. Chemical Biology & Drug Design
- Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases
- (2009) Francesca Milletti et al. Journal of Chemical Information and Modeling
- Comparative Assessment of Scoring Functions on a Diverse Test Set
- (2009) Tiejun Cheng et al. Journal of Chemical Information and Modeling
- Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA
- (2009) Giulio Rastelli et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
- (2009) Mayako Michino et al. NATURE REVIEWS DRUG DISCOVERY
- Investigation of MM-PBSA Rescoring of Docking Poses
- (2008) David C. Thompson et al. Journal of Chemical Information and Modeling
- Structural diversity of G protein-coupled receptors and significance for drug discovery
- (2008) Malin C. Lagerström et al. NATURE REVIEWS DRUG DISCOVERY
- P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
- (2007) Berk Hess Journal of Chemical Theory and Computation
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search