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Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

Tian-ming Zhou, Sheng Wang, Jinbo Xu
doi: https://doi.org/10.1101/240754
Tian-ming Zhou
1Toyota Technological Institute at Chicago, USA
2Department of Computer Science, Tsinghua University, China
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Sheng Wang
3Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Saudi Arabia
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  • For correspondence: jinboxu@gmail.com
Jinbo Xu
1Toyota Technological Institute at Chicago, USA
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  • For correspondence: jinboxu@gmail.com
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Abstract

Intra-protein residue-level contact prediction has drawn a lot of attentions in recent years and made very good progress, but much fewer methods are dedicated to inter-protein contact prediction, which are important for understanding how proteins interact at structure and residue level. Direct coupling analysis (DCA) is popular for intra-protein contact prediction, but extending it to inter-protein contact prediction is challenging since it requires too many interlogs (i.e., interacting homologs) to be effective, which cannot be easily fulfilled especially for a putative interacting protein pair in eukaryotes. We show that deep learning, even trained by only intra-protein contact maps, works much better than DCA for inter-protein contact prediction. We also show that a phylogeny-based method can generate a better multiple sequence alignment for eukaryotes than existing genome-based methods and thus, lead to better inter-protein contact prediction. Our method shall be useful for protein docking, protein interaction prediction and protein interaction network construction.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 28, 2018.
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Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
Tian-ming Zhou, Sheng Wang, Jinbo Xu
bioRxiv 240754; doi: https://doi.org/10.1101/240754
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Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
Tian-ming Zhou, Sheng Wang, Jinbo Xu
bioRxiv 240754; doi: https://doi.org/10.1101/240754

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