Journal ArticleDOI
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review.
TLDR
This review discusses the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline.Abstract:
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.read more
Citations
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Journal ArticleDOI
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
TL;DR: In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed and guidance is provided for practically applying these methods in drug design and related research fields.
Journal ArticleDOI
Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.
TL;DR: Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs.
Journal ArticleDOI
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview.
Veronica Salmaso,Stefano Moro +1 more
TL;DR: An overview of the evolution of structure-based drug discovery techniques in the study of ligand-target recognition phenomenon, going from the static molecular docking toward enhanced molecular dynamics strategies is presented.
Journal ArticleDOI
CB-Dock: a web server for cavity detection-guided protein-ligand blind docking.
TL;DR: A user-friendly blind docking web server, named CB-Dock, is developed, which predicts binding sites of a given protein and calculates the centers and sizes with a novel curvature-based cavity detection approach, and performs docking with a popular docking program, Autodock Vina.
Journal ArticleDOI
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.
TL;DR: Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design and this work presents AutoDockFR–AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoD dock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm and customized scoring function.
References
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Journal ArticleDOI
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
TL;DR: It is shown that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets.
Journal ArticleDOI
New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
TL;DR: A number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens are described.
Journal ArticleDOI
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R. Miller,T. Dwight McGee,Jason M. Swails,Nadine Homeyer,Holger Gohlke,Adrian E. Roitberg +5 more
TL;DR: MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics or Monte Carlo simulations, including the Poisson-Boltzmann Model and several implicit solvation models.
Journal ArticleDOI
ZINC: A Free Tool to Discover Chemistry for Biology
TL;DR: The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets and is freely available at zinc.docking.org.
Journal ArticleDOI
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
TL;DR: An improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC, is described.
Related Papers (5)
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more