pepMMsMIMIC is a public, web-based virtual screening platform with the aim to suggest chemical compounds whose essential elements (pharmacophore) mimic a natural peptide or protein in 3D space which hopefully retain the ability to interact with the biological target and produce the typical biological effect.
Starting from the 3D structure of any protein-protein/peptide complex, pepMMsMIMIC design process begins by identifying the key residues that are responsible for the protein-protein recognition process. In this process, the peptide complexity is reduced and the basic pharmacophore model is defined by its critical structural features (peptide annotation points) in 3D space.
The pepMMsMIMIC paper has been accepted for publication in the NAR Web Server Issue 2011. I will post the Advance Access link in the near future.
Here the abstract:
pepMMsMIMIC is a novel web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers 3D- similarity search strategy. Key to the development of pepMMsMIMIC has been the creation of a library of 17 million conformers calculated from 3.9 million commercially available chemicals collected in the MMsINC® database. Using as input the three-dimensional structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognition of this natural peptide using both pharmacophore and shape similarity techniques. We hope that the accessibility of pepMMsMIMIC will encourage medicinal chemists to de-peptidize protein-protein recognition processes of biological interest, thus increasing the potential of in silico peptidomimetic compound screening of known small molecules to expedite drug development.