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

Software

MM-ISMSA

 

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

 

gCOMBINE

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

 

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.

WikiFred

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

 

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