Detecting Protein Conformational Changes in Interactions via Scaling Known Structures.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

9 Scopus Citations
View graph of relations

Author(s)

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)765-779
Journal / PublicationJournal of computational biology : a journal of computational molecular cell biology
Volume20
Issue number10
Publication statusPublished - Oct 2013

Abstract

Conformational changes frequently occur when proteins interact with other proteins. How to detect such changes in silico is a major problem. Existing methods for docking with conformational changes remain time-consuming, and they solve only a small portion of protein complexes accurately. This work presents a more accurate method (FlexDoBi) for docking with conformational changes. FlexDoBi generates the possible conformational changes of the interface residues that transform the proteins from their unbound states to bound states. Based on the generated conformational changes, multidimensional scaling is performed to construct candidates for the bound structure. We develop a new energy item for determining the orientation of docking subunits and selecting of plausible conformational changes. Experimental results illustrate that FlexDoBi achieves better results. On 20 complexes, we obtained an average iRMSD of 1.55Å, which compares favorably with the average iRMSD of 1.94Å for FiberDock. Compared to ZDOCK, our results are of 0.27Å less in average iRMSD of the medium difficulty group.

Research Area(s)

  • backbone flexibility, database method, energy function, flexible docking, weighted multidimensional scaling

Citation Format(s)

Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. / GUO, FEI; LI, SHUAI CHENG; MA, WENJI; WANG, LUSHENG.

In: Journal of computational biology : a journal of computational molecular cell biology, Vol. 20, No. 10, 10.2013, p. 765-779.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review