Introduction

Understanding proteins' structures and interactions is needed for understanding their mechanisms and hence essential for a complete understanding of life processes at the molecular level. Currently, over seven million protein cases achieve the accuracy of medium-resolution NMR or sequences are deposited in the UniProtKB/TrEMBL database but only 50000 of them have experiment-tally solved structures. The high demand of the community for protein structures has placed computer-based protein structure prediction, the only means to alleviate the problem, at an unprecedentedly crucial position.

However, protein structure prediction needs tremendous computing-time. For instance, threading, the leading methods for protein structure prediction, is exceedingly time-consuming because the query sequence should be aligned to all template in the database. Volunteer computing is absolutely a great chance for protein structure prediction.

This application (SCThread) has implemented an effective threading method based on short-cut phenomenon. Short-cut is frequently observed when two structurally similar proteins are aligned to each other. For these pairs, existing threading methods always fail to identify their structural similarity consequently cannot obtain the optimal alignment. Our method designs a new scoring function which takes short-cut into consideration. Meanwhile, dynamic programming algorithm still can be employed to derive the optimal solution of the scoring function. Comparing with other threading methods, our method can greatly improve the alignment accuracy on short-cut pairs and also performs well on non-short-cut examples.

A next generation of SCThread called ThreeThread is also under development now, and it is expected to be put online before December 1st 2011.

Progress

Thanks all of you! We have obtained very good results on proteins released recently!

Results on 5 Proteins released in CASP9 (2010.12.10)

Thanks to the contribution of all volunteers who support CAS@home, SCThread team has published a paper on BMC Structural Biology in 2011 based on the computing results.( Research Incorporating Ab Initio energy into threading approaches for protein structure prediction : Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Weimou Zheng, Dongbo Bu BMC Bioinformatics 2011, 12(Suppl 1):S54).

Superimpose of the native structure of T0515 and our model