ProtorP: a protein–protein interaction analysis server

• Published in: Bioinformatics Vol. 25; no. 3; pp. 413 - 414
• Main Authors: Reynolds, Christopher, Damerell, David, Jones, Susan
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.02.2009; Oxford Publishing Limited (England)
• Subjects: Binding Sites; Biological and medical sciences; Databases, Protein; Fundamental and applied biological sciences. Psychology; General aspects; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Protein Interaction Mapping - methods; Proteins - chemistry; Proteins - metabolism; Software; User-Computer Interface; Molecular interaction; Analysis; Protein
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btn584

The PROTORP server analyses protein–protein associations in 3D structures. The server calculates a series of physical and chemical parameters of the protein interaction sites that contribute to the binding energy of the association. These parameters include, size and shape, intermolecular bonding, residue and atom composition and secondary structure contributions. The server is flexible, in that it allows users to analyse individual protein associations or large datasets of associations deposited in the PDB, or upload and analyse proprietary files. The properties calculated can be compared with parameter distributions for non-homologous datasets of different classes of protein associations provided on the server website. The server provides an efficient way of characterizing protein–protein associations of new or existing proteins, and a means of putting these values in the context of previously observed associations. Availability: http://www.bioinformatics.sussex.ac.uk/protorp Contact: s.jones@sussex.ac.uk