Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?

A Comparative Approach Linking Molecular Dynamics of Altered Peptide Ligands and MHC with In Vivo Immune Responses

(2010) Bernhard Knapp et al.   PLoS One

The activity of Plasmodium falciparum arginase is mediated by a novel inter-monomer salt-bridge between Glu295-Arg404

(2009) Gordon A. Wells et al.   FEBS Journal

3-Layer-based analysis of peptide–MHC interaction: In silico prediction, peptide binding affinity and T cell activation in a relevant allergen-specific model

(2009) Bernhard Knapp et al.   MOLECULAR IMMUNOLOGY

Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens

(2009) Diana Garzón et al.   MOLECULAR IMMUNOLOGY

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study

(2008) Rakina Yaneva et al.   BIOPOLYMERS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Analysis of key parameters for molecular dynamics of pMHC molecules

(2008) Ulrich Omasits et al.   MOLECULAR SIMULATION

Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna

(2008) Ettore Bismuto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward an atomistic understanding of the immune synapse: Large-scale molecular dynamics simulation of a membrane-embedded TCR–pMHC–CD4 complex

(2007) Shunzhou Wan et al.   MOLECULAR IMMUNOLOGY