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Overview

 
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).

Interface residue definition

CA-CA distance Threshold CA-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.

Deletion file format

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 Threshold CA-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.

    Algorithm parameters