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CRDOCK: another program to dock ligands in macromolecules

CRDOCK is flexible tool to perform docking and virtual screening. The main goal of the program is the speed to be applicable in virtual screening. It implements several sampling (Monte Carlo Simulated Annealing, exhautive search, interaction points matching) and minimization (BFGS, SIMPLEX) algorithms plus some different scoring functions (AMBER force field, ChemScore, Pose/RankScore, Hybrid CRScore) that can be alternated to build a completly different docking tool. The code is dual-licensed, it is open, under the GPLv2 terms for non-comercial academic usage. Comercial users may contact Antonio Morreale for more information and licensing.

The program, also, can be used inside VSDMIP as a docking engine like CDOCK, Autodock, DOCK or Fred.

Important!

We fixed some important bugs that were undermining the program's performance. The new validation results with DUD and ASTEX can be found here. General AUC for the DUD sets is now 0.69 (instead of 0.66) and GPCR set performance (here) has increased to 0.81 from the original 0.67 reported in the article). Early enrichments have been also improved. Additionaly, a new validation using the DUD-E set and an alternative ligand setup (using Confab free generator and MMFF94s charges) can be found here.

Changes since publication:

  • Charge mismatching detection
  • Implicit solvation Model
  • Penzalization for non-interacting groups based on dSASA
  • Filters on ligand properties
  • Several bug fixes (halogens, metals, acceptor-donors typing, etc.)

Brougth to you by

  • Alvaro Cortes Cabrera1,2
  • Federico Gago1
  • Antonio Morreale2*

1Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain 2 Unidad de Bioinformática. Centro de Biología Molecular Severo Ochoa (CSIC-UAM). c/ Nicolás Cabrera 1. Campus de Cantoblanco. Madrid 28049. Spain.

Downloads & Support

Currently we are improving the scoring function to fix some problems we have detected. These improvements will rise the speed and accuracy of the program.

Usage and installation

Documentation and software will be available soon.

Screenshots

HIV protease complexed with JE-2147 (PDB code: 1KZK) and the predicted solution (RMSD: 1.10).

ROC curve of CRDOCK on dihydrofolate reductase with known binders and decoys (dhfr Directory of Useful decoys set, AUC 0.97)

References

  1. 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) Journal of Chemical Information and Modeling (in press)
  2. Cabrera, Á.C.; 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 (2011) Journal of Computer-Aided Molecular Design1-12
Web design: Alfonso Núñez Salgado