BindML: Software for Predicting Protein-Protein Interaction Sites using Phylogenetic Substitution Models

Software for Predicting Protein-Protein Interaction Sites using Phylogenetic Substitution Models

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Reference: D. La and D. Kihara. A novel method for predicting protein-protein interaction sites using phylogenetic substitution models. Proteins: Structure, Function and Bioinformatics. 80: 126-141 (2012).

Instructions for Multiple Sequence Alignment (MSA):
The MSA file you submit must be in the FASTA format and contain the sequence of the PDB structure you supply. Submitting an MSA file is optional. If not submitted, the server will retrieve a MSA from the Pfam database.

Example Input Files:
As an example, you may use Triosephosphate isomerase: 7TIM.pdb (PDB structure), specify chain 'A', and use PF00121.fasta (family MSA).