Poster Presentation 2014 International Biophysics Congress

Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome (#646)

Yuedong Yang 1 , Huiying Zhao 2 , Yaoqi Zhou 1
  1. Institute for Glycomics, Griffith University, Southport, QLD, Australia
  2. QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
Proteins are involved in almost all biological activities and their structures and functions are determined by their one-dimensional amino acids sequences. Since slow and expensive techniques by wet experiments, the annotations of protein structure and function are far behind protein sequencing, especially since the development of next generation sequencing techniques. A practical way to solve this problem is to use computational modeling methods. We developed a new template-based protein structure prediction method SPARKS-X. The method improves the fold recognition by employing probabilistic-based matching between predicted one-dimensional structural properties of query sequence by SPINE-X and corresponding native properties of template structures. This method has been consistently proven to be one of the best methods on different benchmarks. This is further affirmed by its top rank in recent CASP blind tests on structure prediction. Based on SPARKS-X, we have developed a SPOT-Seq package for predicting DNA-binding and RNA-binding proteins by combining it with binding affinity prediction according to a knowledge-based potential function DFIRE. This package enables a genome-wide scanning of DNA-binding and RNA-binding proteins. Beyond making two-state binding or non-binding prediction, the method can also provide a prediction of highly accurate complex structure of protein-DNA and protein-RNA, respectively. These details are extremely informative for experimental biologists.