Deciphering the protein recognition code by integrating physics and statistical analyses
报告人:
王巍
Dept. of Chemistry and Biochemistry, University of California, San Diego
报告时间:
2008-04-25 10:00
报告地点:
理科楼三楼报告厅
主办单位:
物理系
简介:
摘要 Protein-protein interactions play critical roles in almost every biological process. Understanding the mechanism of protein recognition and how the interaction specificity is achieved can greatly help reconstruct protein interaction network and develop therapeutic inhibitors. I will discuss our recent efforts on deciphering the protein recognition code using free energy calculation and classification analyses. We have applied this method to studying the interactions between Src homology 3 (SH3) domain and peptides. These interactions are weak and transient, and they are difficult to be detected by high throughput techniques. We characterized the domain-peptide interaction interface using molecular dynamics simulation and free energy component analysis. We then used a classification algorithm to predict the binding peptides for a given SH3 domain. We assessed the performance of the method using both computational and experimental measurements. Our method achieved significantly higher sensitivity, specificity and prediction accuracy than all the currently available methods. We believe the integration of computer modeling and statistical analyses provides a general framework to decipher the protein recognition code.
