Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

BMC Bioinformatics

Proceedings

Juan Esquivel-Rodríguez¹  Daisuke Kihara² 

[1] Department of Computer Science, College of Science, Purdue University, 47907, West Lafayette, IN, USA;Department of Computer Science, College of Science, Purdue University, 47907, West Lafayette, IN, USA;Department of Biological Sciences, College of Science, Purdue University, 47907, West Lafayette, IN, USA;

关键词: Root Mean Square Deviation;    Protein Structure Prediction;    Pairwise Combination;    Chain Pair;    High Root Mean Square Deviation;   

DOI  :  10.1186/1471-2105-13-S2-S6

来源: Springer

【 摘 要 】

BackgroundMany functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.MethodsWe generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.Results and conclusionWe found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.

【 授权许可】

CC BY   
© Esquivel-Rodríguez and Kihara; licensee BioMed Central Ltd. 2012