Computer-Aided Drug Design | Pharmacometrics | Computational Chemistry/Biology | Chemical Informatics


Antechamber – A Molecular Mechanical Toolkit. To enable accurate MM-based studies, especially in rational drug design, it is critical to develop a set of reliable tools so that force field parameters can be generated for arbitrary molecules accurately and automatically. I developed Antechamber to fulfill this mission. The Antechamber module has been released with AMBER since Version 8. Since then the Antechamber module has been enjoying broad applications both among and outside the AMBER community (there are more than 750 SCI citations, however the number of publications using Antechamber is much higher as most papers only cited the AMBER package instead of the Antechamber module itself). In order to broaden the application of Antechamber and to appropriately cope with the extended chemical space in GAFF2, we are now redeveloping some key Antechamber algorithms. Additional functions such as automatic generation of non-standard residue topologies will be introduced. Web toolkit for MM Calculations. To broaden the application of GAFF and Antechamber, I have developed a web-based toolkit (using MySQL/PHP) to enable users to generate high quality MMFF parameters for arbitrary molecules. I are developing a molecular mechanical model (MMM) database to store MM models for drugs, actives, cofactors and drug-like molecules.