Protein structure prediction and understanding using machine learning methods

Abstract

Summary form only given. The understanding of protein structures is vital to determine the function of a protein and its interaction with DNA, RNA and enzyme. The information about its conformation can provide essential information for drug design and protein engineering. While there are over a million known protein sequences, only a limited number of protein structures are experimentally determined. Hence, prediction of protein structures from protein sequences using computer programs is an important step to unveil proteins' three dimensional conformation and functions. As a result, prediction of protein structures has profound theoretical and practical influence over biological study. In this talk, we would show how to use machine learning methods with various advanced encoding schemes and classifiers improve the accuracy of protein structure prediction. The explanation of how a decision is made is also important for improving protein structure prediction. The reasonable interpretation is not only useful to guide the "wet experiments", but also the extracted rules are helpful to integrate computational intelligence with symbolic AI systems for advanced deduction. Some preliminary results using SVM and decision tree for rule extraction and prediction interpretation would also be presented.