Abstract
BackgroundProtein-protein interface holds important information of protein-protein interactions which play key roles in most biological processes. In the past few years, a lot of efforts have been made to improve interface residue recognition by characterizing protein-protein interfaces and extracting relevant features. However, most previous studies were carried out in a qualitative level, and there are also some inconsistencies between them.ResultsIn the present work, to improve interface residue recognition, we built a novel quantitative residue protein-protein interface propensity index (QIPI) and gained a comprehensive picture of protein-protein interface through analyzing protein-protein interfaces on our comprehensive protein-protein interfaces dataset (Astral2.05-40-4506). Furthermore, in order to assess the effect of QIPI in improving the protein-protein interface prediction, we developed an interface residue recognition method SPR (Single domain based Patch Recognition) based on the QIPI. The evaluation results proved that our novel QIPI is able to improve the interface residue recognition.ConclusionsThrough a comprehensive quantitative analysis of protein-protein interface, we constructed a novel quantitative protein-protein interface propensity index (QIPI), which could be easily applied to improve the interface residue recognition and helpful in understanding the protein-protein interface.AvailabilityQIPI and SPR are available to non-commercial users at our website: http://www.scbit.org/QIPI/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0351-7) contains supplementary material, which is available to authorized users.
Highlights
Availability: quantitative residue interface propensity index (QIPI) and SPR are available to non-commercial users at our website: http://www.scbit.org/QIPI/
Based on the above reason, we constructed the Astral2.05-40 dataset, which is a subset of SCOPe2.05 with less than 40% identity between any two domains, for large-scale analysis of interface propensities
Results we first show the characteristics of protein interfaces in our analysis and develop a novel quantitative residue interface propensity index (QIPI)
Summary
Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence. An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles. Anatomy of hot spots in protein interfaces. ‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces. Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues. Protein–protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. Interaction-site prediction for protein complexes: a critical assessment. Protein-protein interactions play crucial roles in many biological functions [1,2,3]. Various hypotheses have been proposed to delineate the interface architecture and explore the mechanisms of protein-protein interactions. The first study is O-Ring theory which concluded that the existence of a hot-spot enriched region at the center surrounded by an outer ring of non-conserved residues to occlude water [16, 17]
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