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
High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors.
Ting Zhou,Amedeo Caflisch +1 more
TL;DR: A single‐digit micromolar inhibitor of EphB4 with a relatively good selectivity profile is identified in a multimillion‐compound library upon experimental tests of only 23 molecules.
Journal ArticleDOI
Knowledge-based scoring functions in drug design. 1. Developing a target-specific method for kinase-ligand interactions.
TL;DR: The evaluation results clearly demonstrate that a target-specific scoring function is a promising way to improve prediction power in structure-based drug design compared with other general scoring functions.
Journal ArticleDOI
A Comparative Reverse Docking Strategy to Identify Potential Antineoplastic Targets of Tea Functional Components and Binding Mode
TL;DR: The comparative reverse docking strategy presented generates a tractable set of antineoplastic proteins for future experimental validation as drug targets against tumors and provides useful information for studying the antitumor mechanism of tea’s functional components.
Journal ArticleDOI
FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection
Karina S. Machado,Evelyn Koeche Schroeder,Duncan D. Ruiz,Elisângela M L Cohen,Osmar Norberto de Souza +4 more
TL;DR: A work that would usually need the manual execution of many computer programs, and the manipulation of thousands of files, was efficiently and automatically performed by FReDoWS, a Flexible-Receptor Docking Workflow System to automate molecular docking simulations using a fully-flexible receptor model.
Journal ArticleDOI
Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors
TL;DR: A comparative molecular docking study was performed to establish an effective docking protocol for virtual screening of AChE and FRED was found to be the best in reproducing the experimental pose by placing it near the top of its ranking.
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