Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

ABSTRACT: As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions). A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Mat

SUBMITTER: Zhao H 

PROVIDER: S-EPMC4008587 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature