Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII–TCR complex

Predicting peptide vaccine candidates against H1N1 influenza virus through theoretical approaches

(2015) Martiniano Bello et al.   IMMUNOLOGIC RESEARCH

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

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

Understanding the structural dynamics of TCR-pMHC interactions

(2014) Itamar Kass et al.   TRENDS IN IMMUNOLOGY

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

Theoretical analysis of the neuraminidase epitope of the Mexican A H1N1 influenza strain, and experimental studies on its interaction with rabbit and human hosts

(2013) Paola Kinara Reyes Loyola et al.   IMMUNOLOGIC RESEARCH

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

Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space

(2013) Marc Adler et al.   Journal of Chemical Information and Modeling

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

Structure and dynamics of β-lactoglobulin in complex with dodecyl sulfate and laurate: A molecular dynamics study

(2012) Martiniano Bello et al.   BIOPHYSICAL CHEMISTRY

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

(2012) Bernhard Knapp et al.   BMC IMMUNOLOGY

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Signaling at neuro/immune synapses

(2012) Michael L. Dustin   JOURNAL OF CLINICAL INVESTIGATION

Cutting Edge: Evidence for a Dynamically Driven T Cell Signaling Mechanism

(2012) W. F. Hawse et al.   JOURNAL OF IMMUNOLOGY

Molecular Dynamics of a Thermostable Multicopper Oxidase from Thermus thermophilus HB27: Structural Differences between the Apo and Holo Forms

(2012) Martiniano Bello et al.   PLoS One

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

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

Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations

(2011) Athanassios Stavrakoudis   CELL BIOCHEMISTRY AND BIOPHYSICS

Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics

(2011) O. Y. Borbulevych et al.   JOURNAL OF IMMUNOLOGY

Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism

(2011) Daniel R. Scott et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

(2010) Maarten G. Wolf et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2010) Bernhard Knapp et al.   PLoS One

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

T Cell Receptor Cross-reactivity Directed by Antigen-Dependent Tuning of Peptide-MHC Molecular Flexibility

(2009) Oleg Y. Borbulevych et al.   IMMUNITY

Structural immunology and crystallography help immunologists see the immune system in action: How T and NK cells touch their ligands

(2009) Yong Chen et al.   IUBMB LIFE

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

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Conformational changes and flexibility in T-cell receptor recognition of peptide–MHC complexes

(2008) Kathryn M. Armstrong et al.   BIOCHEMICAL JOURNAL

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

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

The Structural Dynamics and Energetics of an Immunodominant T Cell Receptor Are Programmed by Its Vβ Domain

(2008) Jeffrey Ishizuka et al.   IMMUNITY

Analysis of key parameters for molecular dynamics of pMHC molecules

(2008) Ulrich Omasits et al.   MOLECULAR SIMULATION

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

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

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