NPS-HomPPI is a sequence-based non-partner-specific protein-protein interface residue prediction server.
For a given protein sequence, NPS-HomPPI predicts the potential interfaces for this protein based on its k nearest sequence homologs.
User may input query sequence(s)in fasta format. To objectively evaluate NPS-HomPPI, identicial proteins should not be used in making predictions. To acheive that, user may upload a file of proteins that user wants to exclude from making predictions.
The relative solvent accessible area (RASA) ThresholdRASA threshold is to determine a protein residue a surface residue or not. Surface residues are regarded as residues that have RASA at least RASA threshold.
Atom distance ThresholdAtom distance threshold is to determine a surface residue an interface residue or not. An interface residues is a surface residue that has at least one atom within Atom distance threshold from any atoms of residues in another protein chain.
K in K-nearest homologs NPS-HomPPI predicts interface residues in a query protein based on the known interface residues of its K closest homologs in the alignment.
