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

Vaccine Design for CD8 T Lymphocyte Responses

(2013) R. A. Koup et al.   Cold Spring Harbor Perspectives in Medicine

Determinants of public T cell responses

(2012) Hanjie Li et al.   CELL RESEARCH

Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4

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

Prediction of protein-protein binding free energies

(2012) Thom Vreven et al.   PROTEIN SCIENCE

Protein–protein binding affinity prediction on a diverse set of structures

(2011) Iain H. Moal et al.   BIOINFORMATICS

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

T Cell Receptor Signaling Is Limited by Docking Geometry to Peptide-Major Histocompatibility Complex

(2011) Jarrett J. Adams et al.   IMMUNITY

A Role for Differential Variable Gene Pairing in Creating T Cell Receptors Specific for Unique Major Histocompatibility Ligands

(2011) Brian D. Stadinski et al.   IMMUNITY

Tumor Regression in Patients With Metastatic Synovial Cell Sarcoma and Melanoma Using Genetically Engineered Lymphocytes Reactive With NY-ESO-1

(2011) Paul F. Robbins et al.   JOURNAL OF CLINICAL ONCOLOGY

Towards the prediction of protein interaction partners using physical docking

(2011) M. N. Wass et al.   Molecular Systems Biology

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman 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

Large-scale characterization of peptide-MHC binding landscapes with structural simulations

(2011) C. Yanover et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

(2011) Mariana Babor 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

Probing the T-cell receptor repertoire with deep sequencing

(2011) Isabelle Miconnet   Current Opinion in HIV and AIDS

Assessing Energetic Contributions to Binding from a Disordered Region in a Protein−Protein Interaction,

(2010) Sangwoo Cho et al.   BIOCHEMISTRY

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

A New Clustering of Antibody CDR Loop Conformations

(2010) Benjamin North et al.   JOURNAL OF MOLECULAR BIOLOGY

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

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

(2010) Joël Janin   Molecular BioSystems

The autoimmune TCR-Ob.2F3 can bind to MBP85–99/HLA-DR2 having an unconventional mode as in TCR-Ob.1A12

(2010) Zenichiro Kato et al.   MOLECULAR IMMUNOLOGY

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

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

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

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19

(2010) Aroop Sircar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

The Goldilocks Model for TCR—Too Much Attraction Might Not Be Best for Vaccine Design

(2010) Jill E. Slansky et al.   PLOS BIOLOGY

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

(2010) Aroop Sircar et al.   PLoS Computational Biology

Structural alterations in peptide–MHC recognition by self-reactive T cell receptors

(2009) Kai W Wucherpfennig et al.   CURRENT OPINION IN IMMUNOLOGY

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

(2009) Oleg Y. Borbulevych et al.   IMMUNITY

The molecular basis of TCR germline bias for MHC is surprisingly simple

(2009) K Christopher Garcia et al.   NATURE IMMUNOLOGY

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF

(2009) François Ehrenmann et al.   NUCLEIC ACIDS RESEARCH

Evolutionarily Conserved Amino Acids That Control TCR-MHC Interaction

(2008) Philippa Marrack et al.   Annual Review of Immunology

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

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

T-cells behaving badly: structural insights into alloreactivity and autoimmunity

(2008) Lauren K Ely et al.   CURRENT OPINION IN IMMUNOLOGY

Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor

(2008) Angel Varela-Rohena et al.   NATURE MEDICINE

Complete modification of TCR specificity and repertoire selection does not perturb a CD8+ T cell immunodominance hierarchy

(2008) K. Kedzierska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   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