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

Evaluation of peptide selection approaches for epitope-based vaccine design

(2014) B. Schubert et al.   TISSUE ANTIGENS

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

(2013) Sander Pronk et al.   BIOINFORMATICS

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ

(2013) Edita Karosiene et al.   IMMUNOGENETICS

T-cell Receptor Specificity Maintained by Altered Thermodynamics

(2013) Florian Madura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

Structure-Based, Rational Design of T Cell Receptors

(2013) V. Zoete et al.   Frontiers in Immunology

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

(2012) Bernhard Knapp et al.   BMC IMMUNOLOGY

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

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

(2012) Mathias Ferber 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

POPISK: T-cell reactivity prediction using support vector machines and string kernels

(2011) Chun-Wei Tung et al.   BMC BIOINFORMATICS

PeptX: Using Genetic Algorithms to optimize peptides for MHC binding

(2011) Bernhard Knapp et al.   BMC BIOINFORMATICS

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 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

Reliability of 'new drug target' claims called into question

(2011) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

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

(2011) Bernd Rupp et al.   PLoS One

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

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

Prediction of Immunogenicity of Therapeutic Proteins

(2010) Christine J. Bryson et al.   BIODRUGS

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

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

Organization of proximal signal initiation at the TCR:CD3 complex

(2009) Clifford S. Guy et al.   IMMUNOLOGICAL REVIEWS

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

T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity

(2008) Jennifer D. Stone et al.   IMMUNOLOGY

Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases

(2008) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Analysis of key parameters for molecular dynamics of pMHC molecules

(2008) Ulrich Omasits et al.   MOLECULAR SIMULATION

Immune epitope database analysis resource (IEDB-AR)

(2008) Q. Zhang et al.   NUCLEIC ACIDS RESEARCH

Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire

(2008) Sune Frankild et al.   PLoS One

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

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