Mutating, Aligning and Transforming C oordinates Harmonizing Unidentical Proteins

MATCH-UP is a tool to superpose and make proteins similar.

  • Reads two or more PDB files
  • Performs a sequence alignment to generate superposed proteins
  • Makes proteins similar by mutating and deleting residues
  • Outputs standard pdb files compatible for flexible protein docking with FITTED

This program is essential for prepare conformational ensembles for docking with FITTED.

back to top


Protein Rotamers Evaluation and P rotonation based on Accurate Residue Energy

PREPARE is a tool for automated protein preparation and optimization from pdb files directly to mol2 protein and ligand files.

  • Reads PDB files
  • Identifies residues, ligand, co-factors, metals
  • Adds hydrogens
  • Assigns charges, atom types
  • Evaluates rotamers and various protonation states simultaneously
  • Optimizes water molecule orientation
  • Adds particle water molecules accurately NEW
  • Outputs standard mol2 files

PREPARE has originally been reported with the FORECASTER platform and optimized since then.

  • Therrien E., Englebienne P., Arrowsmith A.G., Mendoza-Sanchez R., Corbeil C.R., Weill N., Campagna-Slater V., Moitessier N. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulatorswith FORECASTER, a novel platform for drug discovery Journal of Chemical Information and Modeling (2012), 52, 210-224 link

  • For example, particle water placement and zinc coordinated water and protonation around a zinc ion have been implemented.

  • Therrien E., Weill N., Tomberg A., Corbeil C.R., Lee D., Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy Journal of Chemical Information and Modeling (2014), 54, 3198-3210 link

  • Pottel J., Therrien E., Gleason J.L., Moitessier N. Docking Ligands into Flexible and Solvated Macromolecules. 6. Development and Application to the Docking of HDACs and other Zinc Metalloenzymes Inhibitors Journal of Chemical Information and Modeling (2014), 54, 254-265 link

  • back to top


    Modeling User-defined Transformation Adapting Template Enzyme

    MUTATE is a tool to generate mutants of proteins with optimization of the side chains.

    This program is combined with PREPARE (which adds hydrogen atoms).

    A first version of this program was reported in 2015 while further developments are ongoing.

  • Pottel J., Moitessier N. Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering Journal of Chemical Information and Modeling (2015), 55, 12, 2657-2671 link

  • back to top


    Protein Conformational Ensemble System Setup

    ProCESS is a tool to setup protein files for their use with FITTED.

    This program assigns the advanced residue names, advanced hydrogen names, atom types, and charges for the protein. ProCESS creates interaction sites within the active site cavity. The hydrogen bond donor (HBD), acceptor (HBA) and hydrophobic (HYD) interaction sites are created by locating spheres complementary to the properties of the binding site residues. These interaction sites are used by FITTED for the matching algorithm and the scoring (match score).

    ProCESS has originally been reported with FITTED 1.0 and optimized since then.

  • Corbeil C.R., Englebienne P., Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0 Journal of Chemical Information and Modeling (2007), 47, 435-449 link

  • back to top