Paper Citing NAMD - Abstract
Todman, Sarah J.; Halling-Brown, Mark D.; Davies, Matthew N.; Flower, Darren R.; Kayikci, Melis; Moss, David S.
Toward the atomistic simulation of T cell epitopes Automated construction of MHC: Peptide structures for free energy calculations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 26:957-961, FEB 2008
Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igridext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale. (C) 2007 Elsevier Inc. All rights reserved.
