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Software on drug_design

Software Index


VSDMIP is a platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database.

  • Version : 1.0
  • License : The software is freely distributed for academic and research purposes upon request to the authors.
  • Contact : Antonio Morreale (antonio.morreale@repsol.com)
  • Access : Here
  • References :
    1. Gil-Redondo R, Estrada J, Morreale A, Herranz F, Sancho J, Ortíz AR. VSDMIP: Virtual Screening Data Management on an Integrated Platform J. Comput.-Aided Mol. Design, 23, 171-184 (2009);
    2. Cortés-Cabrera A, Gil-Redondo R, Perona A, Gago F, Morreale A. VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J. Comput.-Aided Mol. Design, 25, 813-824 (2011)[Pubmed]


CRDOCK is a protein-ligand docking program similar to Glide, DOCK or Autodock. It uses a hybrid scoring function based on GlideScore(tm) using a molecular mechanics energy function (AMBER-like) and the ChemScore function to score interactions. The docking program is particularly well suited to generate molecular models of ligand-receptor complexes for further use in COMBINE analysis.

  • Version : 0.8
  • Access : Here.
  • Contact : Antonio Morreale(antonio.morreale@repsol.com)
  • References : Cabrera, A.C.; Klett, J.; Dos Santos, H. G.; Perona, A.; Gil-Redondo, R.; Francis, S. M.; Priegos, E. M.; Gago, F.; Morreale, A.; CRDOCK: An Ultrafast Multipurpose Protein–Ligand Docking Tool (2012) J. Chem. Inf. Model., 52, 2300-20309 (2012)[Pubmed]


A Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics.

  • Version : 0.8
  • Access : Here.
  • Contact : ub@cbm.uam.es
  • References :
    1. Klett J, Núñez-Salgado A, Dos Santos HG, Cortés-Cabrera A, Perona A, Gil-Redondo R, Abia D, Gago F, Morreale A. MM-ISMSA: an ultra-fast and accurate scoring function for protein-protein docking. J. Chem. Theory Comput., 8, 3395-3408 (2012) [Pubmed]

    2. Morreale, A.; Gil-Redondo, R.; Ortiz, A.R. A new implicit solvent model for protein-ligand docking. Proteins 2007 May, 67: 606-16.


A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.

  • Version : 1.2
  • Access : Here.
  • Contact : ub@cbm.uam.es
  • References :
    1. A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Gil-Redondo R,Klett J, Gago F, Morreale A. Proteins 2010; 78(1):162-72
    2. Prediction of drug binding affinities by comparative binding energy analysis. Ortiz AR, Pisabarro MT, Gago F, Wade RC. J Med Chem 1995; 38:2681-91.
    3. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. Perez C, Pastor M, Ortiz AR, Gago F. J Med Chem. 1998:41(6):836-52

cGRILL: a simple affinity map generator

cGRILL calculates 4 affinity maps: lipophilic (CH3), hydrogen bond acceptor (=O), hydrogen bond donor (NH4+) and mixed hydrogen bond donor-acceptor (OH). It implements AMBER force field van der Waals and electrostatic terms and a custom hydrogen bond. The code is not pretty but it is licensed under GPL v3.

Web design: Alfonso Núñez Salgado