PredUs: Prediction of Protein Interfaces Using Structural Alignment
PredUs is a method to predict protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors. Potential interfacial residues are identified by iteratively “mapping” interaction sites of each structural neighbor involved in a complex to individual residues in the query protein (see figure). Residues which frequently have interactions mapped to them are defined to be interfacial.
Please find a full description of the method can in References and information of using PredUs at the webserver Help page.
How to use PredUs
A full description of the method used in PredUs can be found in the following publications.
PredUs is based on an analysis of protein interface conservation:
Zhang QC, Petrey D, Norel R, Honig BH. Protein interface conservation across structure space. Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10896-901. Supplementary Information for the paper.
The PredUs web server was presented with improvements and more benchmarks:
Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 2011;39:W283-W287.
For using PredUs interface prediction in our Markus function annotation server, please cite:
Fisher M, Zhang QC, Deng L, Dey F, Chen BY, Honig B, Petrey D. MarkUs: a server to navigate sequence–structure–function space. Nucleic Acids Res. 2011;39:W357-W361.
PredUs is supported by a funding from the NIH Grant # GM030518, NESG NIH Grant # GM074958 and MAGNet NIH Grant # CA121852.
Developed in the Honig Lab.
For questions about PreUs, contact firstname.lastname@example.org.