PT  - JOURNAL ARTICLE
AU  - Tian-ming Zhou
AU  - Sheng Wang
AU  - Jinbo Xu
TI  - Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
AID  - 10.1101/240754
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 240754
4099  - http://biorxiv.org/content/early/2018/04/28/240754.short
4100  - http://biorxiv.org/content/early/2018/04/28/240754.full
AB  - 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.