Interface analysis servers: Difference between revisions
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The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein and ligand-protein interfaces. | The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein, DNA-protein, RNA-protein, and ligand-protein interfaces. | ||
==COCOMAPS== | ==COCOMAPS== | ||
Revision as of 00:56, 21 February 2012
The purpose of this article is to list and evaluate servers that analyze interfaces within molecular models, such as protein-protein, DNA-protein, RNA-protein, and ligand-protein interfaces.
COCOMAPSCOCOMAPS
COCOMAPS[1] analyzes and visualizes interfaces in biological complexes (such as protein-protein, protein-DNA and protein-RNA complexes). The interface(s) to analyze are specified with the chain identifiers in the PDB file. Output includes three different contact maps, as well as tables reporting detailed information about the interacting residues (defined on the basis of a cut-off distance that can be customized by the user), the residues at the interfaces (defined on the basis of the buried surface upon complex formation), the inter-molecular H-bonds, the buried area, and the interface areas (both as Å2 and percentages).
CommentsComments
- The buried and interfacial areas are not affected by the distance specified when submitting the job.
- Not all interatomic contacts within the specified distance are reported. For example, (February 2012) 4mdh chains A vs. B with a cutoff of 6 Å failed to report (in the Table of Minimum Distances) Tyr 17 CE2 chain A - Arg 237 NH2 chain B, distance 3.89 Å.
ReferencesReferences
- ↑ Vangone A, Spinelli R, Scarano V, Cavallo L, Oliva R. COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes. Bioinformatics. 2011 Oct 15;27(20):2915-6. doi: 10.1093/bioinformatics/btr484., Epub 2011 Aug 27. PMID:21873642 doi:http://dx.doi.org/10.1093/bioinformatics/btr484