Journal ArticleDOI
Latest developments in molecular docking: 2010-2011 in review.
TLDR
The main developments in docking in this period, covered in this review, are receptor flexibility, solvation, fragment docking, postprocessing, docking into homology models, and docking comparisons.Abstract:
The aim of docking is to accurately predict the structure of a ligand within the constraints of a receptor binding site and to correctly estimate the strength of binding. We discuss, in detail, methodological developments that occurred in the docking field in 2010 and 2011, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. The main developments in docking in this period, covered in this review, are receptor flexibility, solvation, fragment docking, postprocessing, docking into homology models, and docking comparisons. Several new, or at least newly invigorated, advances occurred in areas such as nonlinear scoring functions, using machine-learning approaches. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design. Where appropriate, we refer readers to exemplar case studies.read more
Citations
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Journal ArticleDOI
PLIP: fully automated protein–ligand interaction profiler
TL;DR: The protein-ligand interaction profiler (PLIP) is presented, a novel web service for fully automated detection and visualization of relevant non-covalent protein–ligand contacts in 3D structures, freely available at projects.tu-dresden.de/plip-web.
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
DOCK 6: Impact of new features and current docking performance
William J. Allen,Trent E. Balius,Sudipto Mukherjee,Scott R. Brozell,Demetri T. Moustakas,P. Therese Lang,David A. Case,Irwin D. Kuntz,Robert C. Rizzo +8 more
TL;DR: This manuscript presents the latest algorithmic and methodological developments to the structure‐based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry‐corrected root‐mean‐square deviation algorithm, a database filter, and docking forensic tools.
Journal ArticleDOI
Receptor–ligand molecular docking
TL;DR: The main topics and recent computational and methodological advances in protein–ligand docking are summarised, including protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction.
Journal ArticleDOI
Oncogenic protein interfaces: small molecules, big challenges
TL;DR: Some of the latest techniques to discover modulators of protein–protein interactions are described and how current drug discovery approaches have been adapted to successfully target these interfaces are described.
References
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Journal ArticleDOI
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
Rui M.V. Abreu,Rui M.V. Abreu,Hugo J.C. Froufe,Maria João R. P. Queiroz,Isabel C.F.R. Ferreira +4 more
TL;DR: MOLA is an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters and is an ideal virtual screening tool for non-experienced users.
Journal ArticleDOI
Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures
TL;DR: A successful application of the docking of multiple structures to discover novel and potent Chk1 inhibitors and achieving a better enrichment and identifying more diverse compounds was more likely using multiple structures than using only a single structure even when protein structures were randomly selected.
Journal ArticleDOI
Using Free Energy of Binding Calculations to Improve the Accuracy of Virtual Screening Predictions
TL;DR: Free energy rescoring was more accurate than AutoDock4 scores in discriminating between known binders and nonbinders, suggesting free energy rescuing could be a useful approach to reduce false positive predictions in virtual screening experiments.
Journal ArticleDOI
Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.
Sheng-You Huang,Xiaoqin Zou +1 more
TL;DR: Based on a statistical mechanics-based iterative method, a set of distance-dependent, all-atom pairwise potentials for protein-ligand interactions from the crystal structures of 1300 protein- ligand complexes are extracted.
Journal ArticleDOI
Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling
TL;DR: Docking benchmarks reveal that unlike all‐atom docking, Q‐DockLHM exhibits the desired tolerance to the receptor's structure deformation, suggesting that the use of an evolution‐based approach to ligand homology modeling followed by fast low‐resolution refinement is capable of achieving satisfactory performance in ligand‐binding pose prediction with promising applicability to proteome‐scale applications.
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