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PSPT-Protein Structure Prediction Tools

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What's it?

Protein Structure Prediction Tools (PSPT) was built for protein 3D structure prediction. It integrated JiangLab developed four prediction modules , that is, FR-t5-M, CIS-RR, MEFTop, PackingCluster. (1) FR-t5-M is a template based modeling (TBM) method for protein structure prediction. By incorporating MEFTop with our developed threading program FR-t5, the FR-t5-M achieved significant improvement of performance for low-homology protein targets. (2) CISRR couples a novel clash-detection guided iterative search algorithm (CIS) with rotamer relaxation (RR), which removes atomic clashes effectively and achieves high accuracy (about 86% and 76% for Chi1 and Chi1&2, respectively, within 40 degree cutoff). (3) MEFTop is an effective general model evaluation method. Furthermore, the MEFTop could be integrated with traditional threading program to improve the quality of models obviously. (4) PackingCluster present a picture of protein domain organization through an integrated consideration of the arrangements of secondary structure elements (SSE) and residue contact networks.

Link

http://jianglab.ibp.ac.cn:8089/protein

How to use it?

FR-t5-M: in this server, upload a sequence file or paste your sequence on the textbox. After submittion, the prediction result will be sent to your E-mail later. CIS-RR is a user friendly program for accurate prediction of protein side chains and effective elimination of their inner atomic clashes. CISRR could be a very useful tool for subsequent analysis and refinement of protein structures. The MEFTop (Model Evaluation Focused on Topology) is a model quality evaluation program. MEFTop included four groups of features: traditional 1D sequence and 2D residue contact map features, SSE related features, topology features. PackingCluster: after submitting a protein structure file (in PDB format), the packing clusters (also in PDB format) will be calculated and listed on the web page and ready for download.

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