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, DNA-protein, RNA-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. This page does not list ''prediction'' servers. | ||
==COCOMAPS== | ==COCOMAPS== | ||
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*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). | *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== | |||
[http://curie.utmb.edu/prosurf.html InterProSurf] operates on entries in the [[PDB]], or uploaded [[atomic coordinate file]]s. 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== | |||
[http://www.iitm.ac.in/bioinfo/pdbparam/index.html PDBparam] calculates and lists (as text): | |||
#Identifcation of binding sites | |||
#Inter-residue interactions | |||
#Secondary structure propensities | |||
#Physicochemical properties | |||
==LPC/CSU== | ==LPC/CSU== | ||
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==PISA== | ==PISA== | ||
[http://www.ebi.ac.uk/pdbe/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 | [http://www.ebi.ac.uk/pdbe/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 unit]]s 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== | ==See Also== | ||