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
The 5-HT1A Agonism Potential of Substituted Piperazine-Ethyl-Amide Derivatives Is Conserved in the Hexyl Homologues: Molecular Modeling and Pharmacological Evaluation
TL;DR: Docking studies clearly show that hexyl and ethyl compounds favorably interact with the binding site of the active conformation of 5-HT(1A) receptors, thus confirming a possible agonist profile.
Journal ArticleDOI
The ensemble performance index: an improved measure for assessing ensemble pose prediction performance.
TL;DR: A novel interpretable measure, the ensemble performance index (EPI), is introduced, for the assessment of scoring performance in ensemble docking, which will be applied to simulated and real data sets.
Journal ArticleDOI
Evaluation of docking calculations on X-ray structures using CONSENSUS-DOCK.
TL;DR: It is demonstrated that CONSENSUS-DOCK produces better results than DOCK4 for major X-ray structures obtained from the Protein Data Bank (PDB).
Journal ArticleDOI
Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions
TL;DR: The novel internal consensus scoring strategy is an empirical approach with an extended set of 9 binding terms combined with a neural network capable of analysis of diverse complexes capable of maintaining multiple distinct representations of protein-ligand interactions.
Journal ArticleDOI
Chemical Space Sampling in Virtual Screening by Different Crystal Structures
TL;DR: The results show that consensus scoring prioritizes compounds that score moderately against individual crystal structures and is thus complementary to individual crystal structure screening leading to an increase in the diversity of hits.
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