DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles

T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex

(2015) Bernhard Knapp et al.   Journal of Chemical Information and Modeling

MoFvAb: Modeling the Fv region of antibodies

(2015) Alexander Bujotzek et al.   mAbs

Prediction of VH-VL domain orientation for antibody variable domain modeling

(2015) Alexander Bujotzek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DockTope: a Web-based tool for automated pMHC-I modelling

(2015) Maurício Menegatti Rigo et al.   Scientific Reports

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition

(2015) Thomas Hoffmann et al.   PLoS Computational Biology

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes

(2014) Brian G Pierce et al.   BMC BIOINFORMATICS

Subangstrom Accuracy in pHLA-I Modeling by Rosetta FlexPepDock Refinement Protocol

(2014) Tengfei Liu et al.   Journal of Chemical Information and Modeling

Distinct CDR3 Conformations in TCRs Determine the Level of Cross-Reactivity for Diverse Antigens, but Not the Docking Orientation

(2014) L. L. Jones et al.   JOURNAL OF IMMUNOLOGY

Insights into the initiation of TCR signaling

(2014) Arup K Chakraborty et al.   NATURE IMMUNOLOGY

Second antibody modeling assessment (AMA-II)

(2014) Juan C. Almagro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

(2014) Stefan Bietz et al.   Journal of Cheminformatics

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

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor

(2014) Brian G. Pierce 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

EpiDOCK: a molecular docking-based tool for MHC class II binding prediction

(2013) M. Atanasova et al.   PROTEIN ENGINEERING DESIGN & SELECTION

ABangle: characterising the VH-VL orientation in antibodies

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

Rigid Body Energy Minimization on Manifolds for Molecular Docking

(2012) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

A Local Rigid Body Framework for Global Optimization of Biomolecules

(2012) Halim Kusumaatmaja et al.   Journal of Chemical Theory and Computation

A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes

(2012) Brian G. Pierce et al.   PROTEIN SCIENCE

Reconciling views on T cell receptor germline bias for MHC

(2012) K. Christopher Garcia   TRENDS IN IMMUNOLOGY

Vaccines: From Empirical Development to Rational Design

(2012) Christine Rueckert et al.   PLoS Pathogens

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

(2011) Claus Lundegaard et al.   Expert Review of Vaccines

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

(2011) R. L. Warren et al.   GENOME RESEARCH

Structural Basis of Specificity and Cross-Reactivity in T Cell Receptors Specific for Cytochrome c-I-E

(2011) E. W. Newell et al.   JOURNAL OF IMMUNOLOGY

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

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

(2011) Antoine Leimgruber et al.   PLoS One

The diabetogenic mouse MHC class II molecule I-Ag7 is endowed with a switch that modulates TCR affinity

(2010) Kenji Yoshida et al.   JOURNAL OF CLINICAL INVESTIGATION

Allelic polymorphism in the T cell receptor and its impact on immune responses

(2010) Stephanie Gras et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability

(2010) S. R. Burrows et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner

(2009) Kurt H. Piepenbrink et al.   BIOCHEMICAL JOURNAL

The Shaping of T Cell Receptor Recognition by Self-Tolerance

(2009) Stephanie Gras et al.   IMMUNITY

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

(2009) Oleg Y. Borbulevych et al.   IMMUNITY

T Cell Allorecognition via Molecular Mimicry

(2009) Whitney A. Macdonald et al.   IMMUNITY

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

(2009) Travis Beddoe et al.   IMMUNITY

Web application for studying the free energy of binding and protonation states of protein–ligand complexes based on HINT

(2009) Alexander S. Bayden et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition

(2009) Julia K. Archbold et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope

(2009) S. Gras et al.   JOURNAL OF IMMUNOLOGY

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

(2009) Iris Antes   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

(2009) Tobias Lippert et al.   Journal of Cheminformatics

Visualization of unfavorable interactions in protein folds

(2008) C. X. Weichenberger et al.   BIOINFORMATICS

Crossreactive T Cells Spotlight the Germline Rules for αβ T Cell-Receptor Interactions with MHC Molecules

(2008) Shaodong Dai et al.   IMMUNITY

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

(2008) Jeffrey Ishizuka et al.   IMMUNITY

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

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

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC

(2008) Jaafar N. Haidar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR

(2007) Christine McBeth et al.   JOURNAL OF MOLECULAR BIOLOGY