Abstract
Detailed knowledge of interfacial region between interacting proteins is not only helpful in annotating function for proteins, but also very important for structure-based drug design and disease treatment. However, this is one of the most difficult tasks and current methods are constrained by some factors. In this study, we developed a new method to predict residue-residue contacts of two interacting protein domains by integrating information about evolutionary couplings andamino acid pairwise contact potentials, as well as domain-domain interaction interfaces. The experimental results showed that our proposed method outperformed the previous method with the same datasets. Moreover, the method promises an improvement in the source of template-based protein docking.
Highlights
Proteins take part in many biological processes such as DNA replication, gene expression, catalyzing metabolic reactions, and transporting molecules in living cells
We computed coevolution scores and contact potential scores for residue pairs based on direct coupling analysis algorithm [19] and amino acid pairwise contact potentials (AAPCPs) [20], respectively
3) The application of our method enriches the data source for template -based protein docking we attempted to know whether the transfer of posterior interaction probability of residues into Fisher vectors is more effective than directly using posterior interaction probability from the interaction profile hidden Markov model (ipHMM)
Summary
Proteins take part in many biological processes such as DNA replication, gene expression, catalyzing metabolic reactions, and transporting molecules in living cells To implement their functions, proteins often interact with other proteins to form permanent or transient protein complexes. The regions where proteins interact with each other are called protein interfaces The knowledge of these regions is helpful for providing insights into the biological functions of the protein at proteomic level, and for structure-based drug discovery and therapeutics development. Biophysical methods such as NMR (Nuclear Magnetic Resonance) and X-ray crystallography can provide detailed information about structure of protein-protein complexes, but their costs are still high. It is motivated to develop computational methods in characterizing protein-protein interactions (PPIs)
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