Developing new algorithms to rank protein-protein docking decoys


Resolving experimentally the structure of a protein-protein complex still is a complicated task. This has led to the development of docking algorithms for the prediction of the geometry of biomolecular complexes. One of the most important steps is in the selection of the most likely models from an ensemble of possible models. For this purpose we developed a ranking algorithm to select the most likely structures from computer generated docking models.

  • Edrisse Chermak
  • Safwat Abdel-Azeim
      •  CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
          E. Chermak, L. Serra, A. Petta, V. Scarano, R. Oliva, L. Cavallo
          Bioinformatics, In Press, (2014)
      •  Molecular dynamics characterization of five pathogenic factor X mutants associated to decreased catalytic activity
          A.-A. Safwat, R. Oliva, E. Chermak, R. De Cristofaro, L. Cavallo
          Biochemistry, In Press, (2014)
      •  MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
          A.-A. Safwat, E. Chermak, A. Vangone, R. Oliva, L. Cavallo
          BMC Bioinformatics, 15, S1., (2014)