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Pushing the accuracy limit of shape complementarity for protein-protein docking

BACKGROUND: Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representatio...

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Autores principales: Yan, Yumeng, Huang, Sheng-You
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929408/
https://www.ncbi.nlm.nih.gov/pubmed/31874620
http://dx.doi.org/10.1186/s12859-019-3270-y
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author Yan, Yumeng
Huang, Sheng-You
author_facet Yan, Yumeng
Huang, Sheng-You
author_sort Yan, Yumeng
collection PubMed
description BACKGROUND: Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open question in the development of protein-protein docking algorithms, especially for grid-based docking approaches. RESULTS: We have proposed a new pairwise shape-based scoring function (LSC) for protein-protein docking which adopts an exponential form to take into account long-range interactions between protein atoms. The LSC scoring function was incorporated into our FFT-based docking program and evaluated for both bound and unbound docking on the protein docking benchmark 4.0. It was shown that our LSC achieved a significantly better performance than four other similar docking methods, ZDOCK 2.1, MolFit/G, GRAMM, and FTDock/G, in both success rate and number of hits. When considering the top 10 predictions, LSC obtained a success rate of 51.71% and 6.82% for bound and unbound docking, respectively, compared to 42.61% and 4.55% for the second-best program ZDOCK 2.1. LSC also yielded an average of 8.38 and 3.94 hits per complex in the top 1000 predictions for bound and unbound docking, respectively, followed by 6.38 and 2.96 hits for the second-best ZDOCK 2.1. CONCLUSIONS: The present LSC method will not only provide an initial-stage docking approach for post-docking processes but also have a general implementation for accurate representation of other energy terms on grids in protein-protein docking. The software has been implemented in our HDOCK web server at http://hdock.phys.hust.edu.cn/.
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spelling pubmed-69294082019-12-30 Pushing the accuracy limit of shape complementarity for protein-protein docking Yan, Yumeng Huang, Sheng-You BMC Bioinformatics Research BACKGROUND: Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open question in the development of protein-protein docking algorithms, especially for grid-based docking approaches. RESULTS: We have proposed a new pairwise shape-based scoring function (LSC) for protein-protein docking which adopts an exponential form to take into account long-range interactions between protein atoms. The LSC scoring function was incorporated into our FFT-based docking program and evaluated for both bound and unbound docking on the protein docking benchmark 4.0. It was shown that our LSC achieved a significantly better performance than four other similar docking methods, ZDOCK 2.1, MolFit/G, GRAMM, and FTDock/G, in both success rate and number of hits. When considering the top 10 predictions, LSC obtained a success rate of 51.71% and 6.82% for bound and unbound docking, respectively, compared to 42.61% and 4.55% for the second-best program ZDOCK 2.1. LSC also yielded an average of 8.38 and 3.94 hits per complex in the top 1000 predictions for bound and unbound docking, respectively, followed by 6.38 and 2.96 hits for the second-best ZDOCK 2.1. CONCLUSIONS: The present LSC method will not only provide an initial-stage docking approach for post-docking processes but also have a general implementation for accurate representation of other energy terms on grids in protein-protein docking. The software has been implemented in our HDOCK web server at http://hdock.phys.hust.edu.cn/. BioMed Central 2019-12-24 /pmc/articles/PMC6929408/ /pubmed/31874620 http://dx.doi.org/10.1186/s12859-019-3270-y Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Yan, Yumeng
Huang, Sheng-You
Pushing the accuracy limit of shape complementarity for protein-protein docking
title Pushing the accuracy limit of shape complementarity for protein-protein docking
title_full Pushing the accuracy limit of shape complementarity for protein-protein docking
title_fullStr Pushing the accuracy limit of shape complementarity for protein-protein docking
title_full_unstemmed Pushing the accuracy limit of shape complementarity for protein-protein docking
title_short Pushing the accuracy limit of shape complementarity for protein-protein docking
title_sort pushing the accuracy limit of shape complementarity for protein-protein docking
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6929408/
https://www.ncbi.nlm.nih.gov/pubmed/31874620
http://dx.doi.org/10.1186/s12859-019-3270-y
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