Paper Citing NAMD - Abstract
Wallrapp, Frank H.; Guallar, Victor
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:315-322, MAR-APR 2011
Mixed quantum mechanics and molecular mechanics (QM/MM) techniques, wherein the active site is treated with a robust ab initio quantum mechanics methodology and the remainder of the protein is modeled at the molecular mechanics level, offer a valuable tool for looking inside enzymes. We present here a short summary of recent QM/MM applications. We discuss the capabilities of this technology focusing in the main three steps when modeling enzymes: building a model, conformational sampling, and mapping the chemical process. (C) 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 315-322 DOI: 10.1002/wcms.27
