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
Rapid flexible docking using a stochastic rotamer library of ligands
TL;DR: A flexible docking approach, MedusaDock, is proposed, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers, and an algorithm to build the ligand rotamer library "on-the-fly" during docking simulations is developed.
Journal ArticleDOI
Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening
TL;DR: This work systematically assess how multiple crystallographic receptor conformations, a powerful way of discretely representing protein plasticity, can be exploited in screening protocols to separate binders from non-binders.
Journal ArticleDOI
Structure based prediction of subtype-selectivity for adenosine receptor antagonists.
TL;DR: Analysis of the subtype-specific ligand-receptor interactions allowed identification of the major determinants of ligand selectivity, which may facilitate discovery of more efficient drug candidates.
Journal ArticleDOI
A unified, probabilistic framework for structure- and ligand-based virtual screening.
Steven L. Swann,Scott P. Brown,Steven W. Muchmore,Hetal Patel,Philip J. Merta,John Locklear,Philip J. Hajduk +6 more
TL;DR: A unified probabilistic framework for interpreting structure-based virtual screening that returns a quantitative likelihood of observing bioactivity and can be quantitatively combined with ligand-based screening methods to yield a cumulative prediction that consistently outperforms any single screening metric.
Journal ArticleDOI
Consistency properties of species tree inference by minimizing deep coalescences.
Cuong Than,Noah A. Rosenberg +1 more
TL;DR: This article investigates the consistency of the minimizing-deep-coalescence (MDC) criterion and shows that there are indeed anomaly zones for the MDC criterion for asymmetric four-taxon species tree topologies, and for all species treeTopologies with five or more taxa.
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