AN EVOLUTIONARY CONSERVATION-BASED METHOD FOR REFINING AND RERANKING PROTEIN COMPLEX STRUCTURES

BAHAR AKBAL-DELIBAS, IRINA HASHMI, AMARDA SHEHU, NURIT HASPEL
<span title="">2012</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zudjdcas3bcm3lfnfxnjyl5zty" style="color: black;">Journal of Bioinformatics and Computational Biology</a> </i> &nbsp;
Detection of protein complexes and their structures is crucial for understanding their role in the basic biology of organisms. Computational docking methods can provide researchers with a good starting point for the analysis of protein complexes. However, these methods are often not accurate and their results need to be further re¯ned to improve interface packing. In this paper, we introduce a re¯nement method that incorporates evolutionary information into a novel scoring function by employing
more &raquo; ... Evolutionary Trace (ET)-based scores. Our method also takes Van der Waals interactions into account to avoid atomic clashes in re¯ned structures. We tested our method on docked candidates of eight protein complexes and the results suggest that the proposed scoring function helps bias the search toward complexes with native interactions. We show a strong correlation between evolutionary-conserved residues and correct interface packing. Our re¯nement method is able to produce structures with better lRMSD (least RMSD) with respect to the known complexes and lower energies than initial docked structures. It also helps to ¯lter out false-positive complexes generated by docking methods, by detecting little or no conserved residues on false interfaces. We believe this method is a step toward better ranking and prediction of protein complexes.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720012420024">doi:10.1142/s0219720012420024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22809378">pmid:22809378</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bu4zbniycnfennq75cfv5pbgya">fatcat:bu4zbniycnfennq75cfv5pbgya</a> </span>
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