Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Gro2mat: A package to efficiently read gromacs output in MATLAB

(2014) Hung Dien et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study

(2014) Bernhard Knapp et al.   PLoS Computational Biology

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design

(2014) James Dunbar et al.   PLoS Computational Biology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Novel HLA-B27-restricted Epitopes fromChlamydia trachomatisGenerated upon Endogenous Processing of Bacterial Proteins Suggest a Role of Molecular Mimicry in Reactive Arthritis

(2013) Carlos Alvarez-Navarro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential geometric analysis of alterations in MH α-helices

(2013) Birgit Hischenhuber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study

(2013) Amit Kumar et al.   PLoS One

Early Relaxation Dynamics in the LC 13 T Cell Receptor in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study

(2013) Bernhard Knapp et al.   PLoS One

Molecular Dynamics Simulations to Provide Insights into Epitopes Coupled to the Soluble and Membrane-Bound MHC-II Complexes

(2013) Martiniano Bello et al.   PLoS One

ABangle: characterising the VH-VL orientation in antibodies

(2013) J. Dunbar et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Receptor Signaling Clusters in the Immune Synapse

(2012) Michael L. Dustin et al.   Annual Review of Biophysics

Association of HLA-DR1 with the allergic response to the major mugwort pollen allergen: molecular background

(2012) Bernhard Knapp et al.   BMC IMMUNOLOGY

MH2c: Characterization of major histocompatibility α-helices – an information criterion approach

(2012) B. Hischenhuber et al.   COMPUTER PHYSICS COMMUNICATIONS

A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned

(2012) Stephanie Gras et al.   IMMUNOLOGICAL REVIEWS

The structural basis of αβ T-lineage immune recognition: TCR docking topologies, mechanotransduction, and co-receptor function

(2012) Jia-huai Wang et al.   IMMUNOLOGICAL REVIEWS

T-Cell Receptors Binding Orientation over Peptide/MHC Class I Is Driven by Long-Range Interactions

(2012) Mathias Ferber et al.   PLoS One

Modeling and design by hierarchical natural moves

(2012) A. Y. L. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

(2012) Cyril F. Reboul et al.   PLoS Computational Biology

PeptX: Using Genetic Algorithms to optimize peptides for MHC binding

(2011) Bernhard Knapp et al.   BMC BIOINFORMATICS

The Present and Future of Peptide Vaccines for Cancer

(2011) Craig L. Slingluff   CANCER JOURNAL

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

(2011) B. Knapp et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Conformational studies of immunodominant myelin basic protein 1–11 analogues using NMR and molecular modeling

(2011) Despina Laimou et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Dynamical Characterization of Two Differentially Disease Associated MHC Class I Proteins in Complex with Viral and Self-Peptides

(2011) Daniele Narzi et al.   JOURNAL OF MOLECULAR BIOLOGY

The Effect of Mutations on the Alloreactive T Cell Receptor/Peptide–MHC Interface Structure: A Molecular Dynamics Study

(2011) Mikhail Y. Wolfson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules

(2011) Bernd Rupp et al.   PLoS One

TCRep 3D: An Automated In Silico Approach to Study the Structural Properties of TCR Repertoires

(2011) Antoine Leimgruber et al.   PLoS One

How T cell receptors interact with peptide-MHCs: A multiple steered molecular dynamics study

(2011) Michel A. Cuendet et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational Flexibility in Designing Peptides for Immunology: The Molecular Dynamics Approach

(2010) Athanassios Stavrakoudis   Current Computer-Aided Drug Design

Cis-transisomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex

(2010) Athanassios Stavrakoudis   FEBS LETTERS

Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar

(2010) Constanza Cárdenas et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Predicting interactions between T cell receptors and MHC-peptide complexes

(2010) Kirsten Roomp et al.   MOLECULAR IMMUNOLOGY

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

(2010) Bernhard Knapp et al.   PLoS One

Modeling the Ternary Complex TCR-Vβ/CollagenII(261–273)/HLA-DR4 Associated with Rheumatoid Arthritis

(2010) Maria Cristina De Rosa et al.   PLoS One

Antigen Ligation Triggers a Conformational Change within the Constant Domain of the αβ T Cell Receptor

(2009) Travis Beddoe et al.   IMMUNITY

A critical cross-validation of high throughput structural binding prediction methods for pMHC

(2009) Bernhard Knapp et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

(2008) Michel A. Cuendet et al.   BIOPHYSICAL JOURNAL

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

TCR-MHC docking orientation: natural selection, or thymic selection?

(2008) Edward J. Collins et al.   IMMUNOLOGIC RESEARCH

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

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH

Model for the Peptide-Free Conformation of Class II MHC Proteins

(2008) Corrie A. Painter et al.   PLoS One

Side chain substitution benchmark for peptide/MHC interaction

(2008) Bernhard Knapp et al.   PROTEIN SCIENCE

Probing Protein Fold Space with a Simplified Model

(2007) Peter Minary et al.   JOURNAL OF MOLECULAR BIOLOGY

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