Latest developments in molecular docking: 2010-2011 in review.
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...The elimination of false positive results from docking results can be performed using post processing pipelines (22)....
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References
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"Latest developments in molecular do..." refers background or methods in this paper
...New programs tend to be compared with those used widely, and, almost invariably, improvements are claimed: better docking accuracy, more efficient affinity prediction or VS enrichment,([14,17,18,20]) and speedup,([7,9,13,16,19,20]) as well as...
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...Developers of new algorithms (Tables 1 and 2) address different stages and aspects of the docking workflow: posing, optimization,sampling,([13,15,16]) scoring,([14,16,17]) flexibility,([12,13,18]) and automation and parallelization.([19,20]) New programs tend to be compared with those used widely, and, almost invariably, improvements are claimed: better docking accuracy, more efficient affinity prediction or VS enrichment,([14,17,18,20]) and speedup,([7,9,13,16,19,20]) as well as...
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...AutoDock Vina Automation of input and output [19]...
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"Latest developments in molecular do..." refers methods in this paper
...[60] The docking was carried out with Glide, and the estimated binding affinities were correlated with the experimental values....
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...As a highlight of the 2012 developments, the reader is referred to a special issue of JCAMD (2012, volume 26, issue 6), a compendium of papers dedicated to recent advances in and evaluation of the most widely used docking programs (Glide, GOLD, ICM, DOCK, Lead Finder, Surflex-Dock, and HYDE scoring function)....
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...Using docking with Glide (XP and SP), he demonstrated that his method was able to prioritize targets most likely to return lead-like molecules and may be able to identify most tractable pocket(s) on a target....
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...Virtual fragment docking by Glide: a validation study on 190 protein–fragment complexes....
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...[73] The model was trained on sc-PDB (druggable targets from PDB) using the Bayesian approach and was compared with GOLD and Glide in VS against several targets....
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...They were testing GOLD and FlexX predictive abilities using crystal structures of the cytochrome c peroxidase W191G mutant and found that for one particular complex, in silico results disagreed with the experiment....
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...Sotriffer and co-workers tested the structural prediction ability of GOLD and FlexX[67] as a function of consideration of the crystal water molecules in the cavity of the cytochrome c peroxidase W191G mutant....
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...Hui-fang et al. evaluated five inverse docking schemes (GOLD, FlexX, Tarfisdock, TarSearch-X, and TarSearch-M) against a dataset of 1714 structures of 1594 known drug targets covering 18 biochemical functions....
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...Other examples of consensus scoring include VS against kinases;[29] VoteDock development;[17] a combination of quantitative structure–binding affinity relationship (knowledge based) and MedusaScore (force field based);[91] a combination of MCSS and GOLD docking with MM/GBSA rescoring for fragments;[32] a combination of AutoDock4 and AutoDock Vina;[92] a combination of DOCK4,[93] FlexX, and PMF;[94] and HarmonyDOCK....
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...[54] Using GOLD, Glide, FlexX, and Surflex[55] they deconstructed this variability into two independent effects: the inadequacy of the conformational search during docking (major) and random chaotic effects due to sensitivity to (small) input perturbations (minor, but significant)....
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