PS-HomPPI is a homology-based partner-specific protein-protein interface residue prediction server. Given two potential interacting protein sequences, PS-HomPPI predicts the interface residues between these two proteins based on their k nearest homo-interologs (homologous interacting proteins).
CA-CA distance ThresholdCA-CA distance threshold is to determine a residue an interface residue or not. A residue is considered an interfacial residue if its alpha carbon (CA) is within CA-CA distance threshold from the alpha carbon (CA) of any residue in another protein chain.
Users can choose to exclude specific templates from being used by PS-HomPPI when making interface predictions. Here is the acceptable file format:
query_ID1:query_ID2 => pdbID_chainID1:pdbID_chainID2
note:
query_ID1 and query_ID2 have to be the same as used in the list of query ID pairs and the fasta file.
query_IDs are "freely" named by the users. No space and specially characters should be included.
template IDs have to follow the format of pdbID_chainID.
=> has to be used to separate query and template IDs.
For example,
1a2kA:1a2kC =>
1a14H:1a14N => 1NMBH:1NMBN,1A14H:1A14N,1NMAH:1NMAN
A:B => 1NMBH:1NMBN,1NMAH:1NMAN
C:D => 3fclB:*,1lqmA:*
qry1:qry2 => 3fcl*
CatS:FeB => 3fcl*:3fcl*
E:F => 3fclA:3fcl*
For the query pair 1a2kA:1a2kC, no templates are excluded.
For the query pair 1a14H:1a14N, 3 templates are excluded.
For the query pair A:B, wildcards are used. This means that all dimer templates that include 3fcl_B or 1lqm_A are excluded.
CA-CA distance ThresholdCA-CA distance threshold is to determine a residue an interface residue or not. A residue is considered an interfacial residue if its alpha carbon (CA) is within CA-CA distance threshold from the alpha carbon (CA) of any residue in another protein chain.
