Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations

Sarah J. Todman, Mark D. Halling-Brown, Matthew N. Davies, Darren R Flower, Melis Kayikci, David S. Moss

Research output: Contribution to journalArticlepeer-review


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 ( allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.
Original languageEnglish
Pages (from-to)957-961
Number of pages5
JournalJournal of Molecular Graphics and Modelling
Issue number6
Early online date28 Jul 2007
Publication statusPublished - Feb 2008


  • T cell epitopes
  • MHC molecules
  • homology modelling
  • molecular dynamics
  • free energy calculations


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