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== | ||
