Computational protocol: Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces

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Protocol publication

[…] An initial list of 17,658 binary interfaces was retrieved from the InterEvol resource [] (http://biodev.cea.fr/interevol/downloads.html). This list is non-redundant at the dimer level, at the 70% threshold. We termed this list DIMER70. In this list, interfaces are already annotated in terms of:heterodimer or homodimer complexes,obligate or non-obligate complexes (predicted by NOXclass []),biological interfaces or crystal contacts (predicted by NOXclass).We further made the distinction between interfaces extracted from complexes with two chains (dimers) and those extracted from higher order complexes (K-mers), from information available in the PDB.We filtered the DIMER70 list in order to reduce the redundancy between monomers to 25%, using PISCES (http://dunbrack.fccc.edu/PISCES.php) [] with the following input parameters: sequence percentage identity <25%, resolution <3Å, R-factor <0.3, sequence length between 40 and 10,000, include non-X-ray structures, exclude CA-only structures, Cull PDB by chain. The filtered list contains 5203 monomers and is termed MONOMER25. […]

Pipeline specifications

Software tools NOXclass, PISCES
Application Protein interaction analysis