Interface analysis servers
From Proteopedia
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. This page does not list prediction servers.
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COCOMAPS
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).
Comments
- The buried and interfacial areas are not affected by the distance specified when submitting the job.
- Note that the Table of minimum distances lists only the minimum interatomic distance for each pair of residues, not all interatomic distances. The list of all can be obtained by clicking Open table under Distance table. However it is not filterable or sortable at the time of this writing (March, 2012).
- Residue counts and inter-atomic distances are tabulated, but neither surface nor interfacial atom counts (in contrast to PISA).
InterProSurf
InterProSurf operates on entries in the PDB, or uploaded atomic coordinate files. Reports numbers of surface and buried atoms for each chain, and areas for each residue deemed to be in the interface. Terms are not defined or explained.
PDBparam
PDBparam calculates and lists (as text):
- Identifcation of binding sites
- Inter-residue interactions
- Secondary structure propensities
- Physicochemical properties
LPC/CSU
The Ligand-Protein Contacts & Contacts of Structural Units server was not working when tested in January, 2015.
PDBsum
Every PDB structure page in Proteopedia links to PDBsum under the structure window where it says 'Resources'. The PDBsum page for every structure includes pre-calculated data summarizing protein-protein interactions and buried surface area, salt bridges, disulfide bonds, hydrogen bonds, and non-bonded contacts; protein-nucleic acid, ligand interactions and available clefts, among other data. The data are accessible via links at the top where you will see 'Prot-prot', 'Ligands', 'Clefts,' etc. depending upon what is available. Note that the protein-nucleic acid interactions, if present, will be found on the page that is accessible via the 'DNA/RNA' link — there will be a link for the NUCPLOT data.
It is also possible to upload your own data and get a similar report generated that contains this information.
PISA
The PISA server (Proteins, Interfaces, Structures and Assemblies), is also termed PDBePISA. Entries in the PDB are pre-calculated, or you can upload your own atomic coordinate file. PISA analyses interfaces occurring in asymmetric units and also predicts probable quaternary structures based on interactions occurring in the macromolecular crystal. Its pre-calculated database is searchable. Click on a row number to see full details for any interacting pair of entities. For each chain in a pair of contacting chains, or ligand-chain interaction, it reports total surface area, interfacial area, numbers and percentages of atoms and residues on the surface and in the interface, and numbers of disulfide and hydrogen bonds and salt bridges in the interface, and interfacial free energy changes. There is also an annotated list of all residues in each chain.
Most terms are defined with pop-up boxes, but methods are not described on the website.
Details are reported only for pairs of entities. If one wanted to know the total number of contacting atoms on one chain that is contacting multiple other chains, one would have to add them up manually.
See Also
References
- ↑ 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. Epub 2011 Aug 27. PMID: 21873642
