How good is automated protein docking
Dima Kozakov,Dmitri Beglov,Tanggis Bohnuud,Scott E. Mottarella,Bing Xia,David R. Hall,Sandor Vajda +6 more
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TLDR
This article evaluates the performance of ClusPro 2.0 for targets 46–58 in Rounds 22–27 of CAPRI and confirms that ranking models based on cluster size can reliably identify the best near‐native conformations.Abstract:
The protein docking server ClusPro has been participating in critical assessment of prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the performance of ClusPro 2.0 for targets 46-58 in Rounds 22-27 of CAPRI. The analysis leads to a number of important observations. First, ClusPro reliably yields acceptable or medium accuracy models for targets of moderate difficulty that have also been successfully predicted by other groups, and fails only for targets that have few acceptable models submitted. Second, the quality of automated docking by ClusPro is very close to that of the best human predictor groups, including our own submissions. This is very important, because servers have to submit results within 48 h and the predictions should be reproducible, whereas human predictors have several weeks and can use any type of information. Third, while we refined the ClusPro results for manual submission by running computationally costly Monte Carlo minimization simulations, we observed significant improvement in accuracy only for two of the six complexes correctly predicted by ClusPro. Fourth, new developments, not seen in previous rounds of CAPRI, are that the top ranked model provided by ClusPro was acceptable or better quality for all these six targets, and that the top ranked model was also the highest quality for five of the six, confirming that ranking models based on cluster size can reliably identify the best near-native conformations.read more
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Journal ArticleDOI
The ClusPro web server for protein-protein docking.
Dima Kozakov,David R. Hall,Bing Xia,Kathryn A. Porter,Dzmitry Padhorny,Christine Yueh,Dmitri Beglov,Sandor Vajda +7 more
TL;DR: This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results of the ClusPro server.
Journal ArticleDOI
Software for molecular docking: a review
TL;DR: Docking against homology-modeled targets also becomes possible for proteins whose structures are not known, and the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes.
Journal ArticleDOI
SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2.
Thomas Mandel Clausen,Thomas Mandel Clausen,Thomas Mandel Clausen,Daniel R. Sandoval,Charlotte B Spliid,Charlotte B Spliid,Charlotte B Spliid,Jessica Pihl,Jessica Pihl,Jessica Pihl,Hailee R. Perrett,Chelsea D. Painter,Anoop Narayanan,Sydney A. Majowicz,Elizabeth M. Kwong,Rachael N. McVicar,Bryan E. Thacker,Charles A. Glass,Zhang Yang,Jonathan L. Torres,Gregory J. Golden,Phillip L. Bartels,Ryan N. Porell,Aaron F. Garretson,Logan K. Laubach,Jared Feldman,Xin Yin,Yuan Pu,Blake M. Hauser,Timothy M. Caradonna,Benjamin P. Kellman,Cameron Martino,Philip L.S.M. Gordts,Sumit K. Chanda,Aaron G. Schmidt,Aaron G. Schmidt,Kamil Godula,Sandra L Leibel,Joyce Jose,Kevin D. Corbett,Andrew B. Ward,Aaron F. Carlin,Jeffrey D. Esko +42 more
TL;DR: A model in which viral attachment and infection involves heparan sulfate-dependent enhancement of binding to ACE2 is suggested, in which Manipulation of hepara sulfate or inhibition of viral adhesion by exogenous heparin presents new therapeutic opportunities.
Journal ArticleDOI
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik,Dominik Gront,Michal Kolinski,Lukasz Wieteska,Lukasz Wieteska,Aleksandra Elzbieta Dawid,Andrzej Kolinski +6 more
TL;DR: An overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions are provided.
Journal ArticleDOI
New additions to the ClusPro server motivated by CAPRI.
Sandor Vajda,Christine Yueh,Dmitri Beglov,Tanggis Bohnuud,Scott E. Mottarella,Bing Xia,David R. Hall,Dima Kozakov +7 more
TL;DR: An extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs that will further improve the utility of ClusPro.
References
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