POPSCOMP
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Server Version 1.1.2; POPS* Version 1.5.3
Overview
POPSCOMP is a method to analyse complexes of proteins and/or nucleic acids.
The interaction between the individual complex components is assessed by
calculating the solvent accessible surface area (SASA) buried upon complex formation.
An example for an application of complex analysis is given in
Fraternali, F. and Cavallo, L. (2002).
POPSCOMP applies the POPS* method, which has its own
POPS* server.
POPSCOMP computes internally the SASA differences between complex components in isolated and paired form. A component is by default a chain, assuming that the complex is formed by separate chains. Alternatively the domain information of the PFAM database can be used and chains are automatically replaced by domains as components (input option 'Domain' will be added soon).
Note that the computational load scales with n^2 (n: number of components) and the total number of allowed components is limited to 20. If less than 2 or more than 20 components are contained in the given structure the program exits with the following error message: 'Error: Too few/many components in input file'. POPSCOMP calculation will be performed on the first model only, if a structure file containing multiple models is submitted.
After submission a holding page provides access to the result page. Otherwise results (also of previous runs) can be accessed through the Retrieve function.
Users publishing results obtained with the POPSCOMP server should acknowledge its use by the following citations: Fraternali, F. and Cavallo, L. (2002) and Kleinjung, J. and Fraternali, F. (2005).
References
-
Fraternali, F. and van Gunsteren, W.F.
An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
Journal of Molecular Biology 256 (1996) 939-948. [PubMed Abstract] -
Fraternali, F. and Cavallo, L.
Parameter optimized surfaces (POPS*): analysis of key interactions and conformational changes in the ribosome.
Nucleic Acids Research 30 (2002) 2950-2960. [PDF] -
Cavallo, L., Kleinjung, J. and Fraternali, F.
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.
Nucleic Acids Research 31 (2003) 3364-3366. [PDF] -
Kleinjung, J. and Fraternali, F.
POPSCOMP: an automated interaction analysis of biomolecular complexes.
Nucleic Acids Research 33 (2005) W342-W346. [PDF]
The POPSCOMP server was developed by Franca Fraternali and Jens Kleinjung, the POPSCOMP logo was designed by Domenico Fraternali. Contact Authors
