VSDMIP
VSDMIP es una plataforma para el cribado virtural
de quimiotecas, integrada en una base de datos relacional MySQL.
- Versión : 1.0
- Licencia : La plataforma se distribuye gratuitamente para uso académico y de investigación, bajo petición a los authores.
- Contactar con : Antonio Morreale (antonio.morreale@repsol.com)
- Acceso : Aquí
- Referencia :
- 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);
- 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
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.
- Versión : 0.8
- Acceso : Aquí.
- Contactar con : Antonio Morreale(antonio.morreale@repsol.com)
- Referencia :
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]
MM-ISMSA
A Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics.
- Versión : 0.8
- Acceso : Aquí.
- Contactar con : ub@cbm.uam.es
- Referencia :
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]
Morreale, A.; Gil-Redondo, R.; Ortiz, A.R.
A new implicit solvent model for protein-ligand docking.
Proteins 2007 May, 67: 606-16.
gCOMBINE
A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes.
- Versión : 1.2
- Acceso : Aquí.
- Contactar con : ub@cbm.uam.es
- Referencia :
- 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
- 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.
- 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.