Optimal contact map alignment of protein-protein interfaces.

Bioinformatics
Vinay PulimJadwiga Bienkowska

Abstract

The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here, we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enh...Continue Reading

References

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Dec 22, 2007·Protein Science : a Publication of the Protein Society·Vinay PulimBonnie Berger

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Citations

Jul 14, 2010·Bioinformatics·Mu Gao, Jeffrey Skolnick
Jul 4, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Romina OlivaLuigi Cavallo
Jun 2, 2009·Current Opinion in Structural Biology·Hitomi Hasegawa, Liisa Holm
Dec 9, 2014·Israel Journal of Chemistry·Jeffrey SkolnickHongyi Zhou
Mar 6, 2015·Proteins·James D Alsop, Julie C Mitchell
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Bin PangChi-Ren Shyu
Apr 12, 2014·Current Opinion in Structural Biology·Andras Szilagyi, Yang Zhang
Jun 3, 2015·Journal of Chemical Information and Modeling·Florian KrullErnst-Walter Knapp
Sep 18, 2014·Frontiers in Genetics·Giovanni MicaleAlfredo Ferro

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Software Mentioned

MUSCLE
LTHREADER
CMAPi
MAPPIS
CLUSTALW

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