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
More filters
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
More filters
Journal ArticleDOI
A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors.
TL;DR: SAR among inhibitors was investigated, which revealed that the oxo group of pyrazolopyrimidine analogs is essential for its activity and the tricyclic derivatives are shown to be more potent than bicyclic ones.
Journal ArticleDOI
LigDockCSA: protein-ligand docking using conformational space annealing.
Woong-Hee Shin,Lim Heo,Lim Heo,Juyong Lee,Juyong Lee,Junsu Ko,Junsu Ko,Chaok Seok,Chaok Seok,Jooyoung Lee +9 more
TL;DR: It is shown that the CSA search method can find lower energy binding poses than the Lamarckian genetic algorithm of AutoDock, however, lower‐energy solutions CSA produced with the AutoDocking energy were often less native‐like.
Journal ArticleDOI
PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements
Yat T. Tang,Garland R. Marshall +1 more
TL;DR: Evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development suggests that using high- resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.
Journal ArticleDOI
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening.
TL;DR: The recently developed FINDSITE/Q-Dock ligand homology modeling approach is employed, which is well-suited for proteome-scale applications using predicted structures, to provide extensive structural and functional characterization of the human kinome.
Journal ArticleDOI
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
TL;DR: The results elucidate the importance of bridging water molecules at the GSK3β‐inhibitor interfaces and suggest that they might prove useful in rational drug design.
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