FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network.

Briefings in Bioinformatics
Jiangyi ShaoBin Liu

Abstract

As a key for studying the protein structures, protein fold recognition is playing an important role in predicting the protein structures associated with COVID-19 and other important structures. However, the existing computational predictors only focus on the protein pairwise similarity or the similarity between two groups of proteins from 2-folds. However, the homology relationship among proteins is in a hierarchical structure. The global protein similarity network will contribute to the performance improvement. In this study, we proposed a predictor called FoldRec-C2C to globally incorporate the interactions among proteins into the prediction. For the FoldRec-C2C predictor, protein fold recognition problem is treated as an information retrieval task in nature language processing. The initial ranking results were generated by a surprised ranking algorithm Learning to Rank, and then three re-ranking algorithms were performed on the ranking lists to adjust the results globally based on the protein similarity network, including seq-to-seq model, seq-to-cluster model and cluster-to-cluster model (C2C). When tested on a widely used and rigorous benchmark dataset LINDAHL dataset, FoldRec-C2C outperforms other 34 state-of-the-art meth...Continue Reading

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Citations

Nov 3, 2020·Computational and Mathematical Methods in Medicine·Zhiyu TaoYuming Zhao
Nov 3, 2020·Computational and Mathematical Methods in Medicine·Qingwen LiLichao Zhang
Mar 16, 2021·Frontiers in Bioengineering and Biotechnology·Yifan ChenLinlin Zhuo
Apr 20, 2021·Frontiers in Genetics·Yuanyuan LvBo Gao
Jul 9, 2021·Frontiers in Genetics·Lei XuRong Song
Jul 3, 2021·Mathematical Biosciences and Engineering : MBE·Hasan ZulfiqarRenzhi Cao
Jun 24, 2021·BioMed Research International·Yanjuan LiZhixia Teng
Jul 1, 2021·Briefings in Functional Genomics·Xiaoqing RuChen Lin

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Methods Mentioned

BETA
feature extraction
seq-to-seq

Software Mentioned

SSHMM
SP4
CMsearch
BLAST
SPARKS
BLASTLINK
Gephi
HMMER
THREADER
HH

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