Maybe.... Nat Protoc.<http://www.ncbi.nlm.nih.gov/pubmed?term=Predicting%20protein-protein%20interactions%20on%20a%20proteome%20scale%20by%20matching%20evolutionary%20and%20structural%20similarities%20at%20interfaces%20using%20PRISM#> 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structuralsimilarities at interfaces using PRISM. Tuncbag N<http://www.ncbi.nlm.nih.gov/pubmed?term=Tuncbag%20N%5BAuthor%5D&cauthor=true&cauthor_uid=21886100>, Gursoy A<http://www.ncbi.nlm.nih.gov/pubmed?term=Gursoy%20A%5BAuthor%5D&cauthor=true&cauthor_uid=21886100>, Nussinov R<http://www.ncbi.nlm.nih.gov/pubmed?term=Nussinov%20R%5BAuthor%5D&cauthor=true&cauthor_uid=21886100>, Keskin O<http://www.ncbi.nlm.nih.gov/pubmed?term=Keskin%20O%5BAuthor%5D&cauthor=true&cauthor_uid=21886100>. Source Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, Sariyer Istanbul, Turkey. Abstract Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions bystructural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs.PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately,PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.
On 8 Aug 2012, at 07:33, Careina Edgooms wrote: Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina Roberto Steiner Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 [email protected]<mailto:[email protected]>
