How to use not-always-reliable binding site information in protein-protein docking prediction.

In many protein-protein docking algorithms, binding site information is used to help predicting the protein complex structures. Using correct and accurate binding site information can increase protein-protein docking success rate significantly. On the other hand, using wrong binding sites informatio...

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Main Authors: Lin Li, Yanzhao Huang, Yi Xiao
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2013-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3790831?pdf=render
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spelling doaj-7e4959415e22412d88af1d846dc6adf02020-11-24T21:16:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01810e7593610.1371/journal.pone.0075936How to use not-always-reliable binding site information in protein-protein docking prediction.Lin LiYanzhao HuangYi XiaoIn many protein-protein docking algorithms, binding site information is used to help predicting the protein complex structures. Using correct and accurate binding site information can increase protein-protein docking success rate significantly. On the other hand, using wrong binding sites information should lead to a failed prediction, or, at least decrease the success rate. Recently, various successful theoretical methods have been proposed to predict the binding sites of proteins. However, the predicted binding site information is not always reliable, sometimes wrong binding site information could be given. Hence there is a high risk to use the predicted binding site information in current docking algorithms. In this paper, a softly restricting method (SRM) is developed to solve this problem. By utilizing predicted binding site information in a proper way, the SRM algorithm is sensitive to the correct binding site information but insensitive to wrong information, which decreases the risk of using predicted binding site information. This SRM is tested on benchmark 3.0 using purely predicted binding site information. The result shows that when the predicted information is correct, SRM increases the success rate significantly; however, even if the predicted information is completely wrong, SRM only decreases success rate slightly, which indicates that the SRM is suitable for utilizing predicted binding site information.http://europepmc.org/articles/PMC3790831?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Lin Li
Yanzhao Huang
Yi Xiao
spellingShingle Lin Li
Yanzhao Huang
Yi Xiao
How to use not-always-reliable binding site information in protein-protein docking prediction.
PLoS ONE
author_facet Lin Li
Yanzhao Huang
Yi Xiao
author_sort Lin Li
title How to use not-always-reliable binding site information in protein-protein docking prediction.
title_short How to use not-always-reliable binding site information in protein-protein docking prediction.
title_full How to use not-always-reliable binding site information in protein-protein docking prediction.
title_fullStr How to use not-always-reliable binding site information in protein-protein docking prediction.
title_full_unstemmed How to use not-always-reliable binding site information in protein-protein docking prediction.
title_sort how to use not-always-reliable binding site information in protein-protein docking prediction.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2013-01-01
description In many protein-protein docking algorithms, binding site information is used to help predicting the protein complex structures. Using correct and accurate binding site information can increase protein-protein docking success rate significantly. On the other hand, using wrong binding sites information should lead to a failed prediction, or, at least decrease the success rate. Recently, various successful theoretical methods have been proposed to predict the binding sites of proteins. However, the predicted binding site information is not always reliable, sometimes wrong binding site information could be given. Hence there is a high risk to use the predicted binding site information in current docking algorithms. In this paper, a softly restricting method (SRM) is developed to solve this problem. By utilizing predicted binding site information in a proper way, the SRM algorithm is sensitive to the correct binding site information but insensitive to wrong information, which decreases the risk of using predicted binding site information. This SRM is tested on benchmark 3.0 using purely predicted binding site information. The result shows that when the predicted information is correct, SRM increases the success rate significantly; however, even if the predicted information is completely wrong, SRM only decreases success rate slightly, which indicates that the SRM is suitable for utilizing predicted binding site information.
url http://europepmc.org/articles/PMC3790831?pdf=render
work_keys_str_mv AT linli howtousenotalwaysreliablebindingsiteinformationinproteinproteindockingprediction
AT yanzhaohuang howtousenotalwaysreliablebindingsiteinformationinproteinproteindockingprediction
AT yixiao howtousenotalwaysreliablebindingsiteinformationinproteinproteindockingprediction
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