Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information

BMC Bioinformatics

Research

Gajendra PS Raghava¹  Nitish K Mishra¹ 

[1] Institute of Microbial Technology, Sector 39A, Chandigarh, INDIA;

关键词: Support Vector Machine;    Area Under Curve;    Support Vector Machine Model;    Flavin Adenine Dinucleotide;    Evolutionary Information;   

DOI  :  10.1186/1471-2105-11-S1-S48

来源: Springer

【 摘 要 】

BackgroundFlavin binding proteins (FBP) plays a critical role in several biological functions such as electron transport system (ETS). These flavoproteins contain very tightly bound, sometimes covalently, flavin adenine dinucleotide (FAD) or flavin mono nucleotide (FMN). The interaction between flavin nucleotide and amino acids of flavoprotein is essential for their functionality. Thus identification of FAD interacting residues in a FBP is an important step for understanding their function and mechanism.ResultsIn this study, we describe models developed for predicting FAD interacting residues using 15, 17 and 19 window pattern. Support vector machine (SVM) based models have been developed using binary pattern of amino acid sequence of protein and achieved maximum accuracy 69.65% with Mathew's Correlation Coefficient (MCC) 0.39 and Area Under Curve (AUC) 0.773. The performance of these models have been improved significantly from 69.65% to 82.86% with MCC 0.66 and AUC 0.904, when evolutionary information is used as input in SVM. The evolutionary information was generated in form of position specific score matrix (PSSM) profile by using PSI-BLAST at e-value 0.001. All models were developed on 198 non-redundant FAD binding protein chains containing 5172 FAD interacting residues and evaluated using fivefold cross-validation technique.ConclusionThis study suggests that evolutionary information of 17 amino acid patterns perform best for FAD interacting residues prediction. We also developed a web server which predicts FAD interacting residues in a protein which is freely available for academics.

【 授权许可】

CC BY   
© Mishra and Raghava; licensee BioMed Central Ltd. 2010