Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong

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Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

RDbBMC bioinformatics · 2020
Article

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5 · Who and what money

Authors and funding

4 authors.

Wenzhi MaoMOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.

Tong WangMOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.

Wenxuan ZhangMOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.

Haipeng GongMOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China. hgong@tsinghua.edu.cn.ORCID 0000-0002-5532-1640

Funding

National Natural Science Foundation of China (CN) 31621092National Natural Science Foundation of China (CN) 31670723

6 · The paper itself

Abstract

backgroundDespite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map.

resultsOur algorithm RDb

conclusionOur method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. AVAILABILITY: All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

Indexed as

AlgorithmsAmino AcidsComputational BiologyModels, MolecularProtein Conformation, beta-StrandProteinsProtein Structure, TertiaryReproducibility of ResultsAmino AcidsProteinsContact mapProtein structure predictionRandom forestResidue contact predictionRidge detectionβ-β pairing

Identifiers

PMID29673311

DOI10.1186/s12859-018-2150-1

PMCPMC5907701

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