Welcome to the website (under permanent construction) of the Molecular Modeling Lab of the University of Alcalá (Spain).




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



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



cGRILL: an unsophisticated 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.




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.


Here you can find some tricks that worked for us and can make your life as a Computational Scientist easier :)