List of works - Brian M. Baker

2064: Deconstructing the peptide specificity of TCR recognition

3348 Structural Determinants of Neoantigen Immunogenicity for Cancer Therapy

4322 Structure-guided design of the TIL1383I T cell receptor

scientific article

A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves

scientific article published on October 2009

A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces

scientific article

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.

scientific article published on 3 February 2017

Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells

scientific article published on 2 February 2018

An Amino Acid Position at Crossroads of Evolution of Protein Function: ANTIBIOTIC SENSOR DOMAIN OF BlaR1 PROTEIN FROM STAPHYLOCOCCUS AUREUS VERSUS CLASS D -LACTAMASES

scientific article

An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.

scientific article published on 24 May 2016

An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes

scientific article published on 19 October 2020

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection

scientific article published on 15 December 2020

Changing the peptide specificity of a human T-cell receptor by directed evolution.

scientific article

Citizens unite for computational immunology!

scientific article

Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

scientific article

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

scientific article

Computational Modeling of T Cell Receptor Complexes

scientific article published on 01 January 2016

Computational Reprogramming of T Cell Antigen Receptor Binding Properties

scientific article published in January 2016

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

scientific article published on January 31, 2011

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

scientific article published on October 2008

Correction to: Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

scientific article published on 20 December 2017

Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells

scientific article published on 20 June 2017

Crystal Structures of HLA-A*0201 Complexed with Melan-A/MART-1 26(27L)-35 Peptidomimetics Reveal Conformational Heterogeneity and Highlight Degeneracy of T Cell Recognition

scientific article

Cutting edge: Evidence for a dynamically driven T cell signaling mechanism.

scientific article

Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex

scientific article

Design, synthesis and evaluation of β-lactam antigenic peptide hybrids; unusual opening of the β-lactam ring in acidic media ⬇️

scientific article published on October 7, 2010

Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes

scientific article published on 18 February 2016

Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity

scientific article published on 27 April 2016

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

scientific article published on October 12, 2011

Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility

scientific article published on 03 May 2019

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes

scientific article published in October 2017

Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity

scientific article

FOXO3-NF-κB RelA Protein Complexes Reduce Proinflammatory Cell Signaling and Function

scientific article

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

scientific article

Full-length influenza hemagglutinin HA2 refolds into the trimeric low-pH-induced conformation

scientific article published in May 2004

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

scientific article

Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen

scientific article published on 21 October 2019

Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability

scientific article

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides

scientific article published on 23 December 2020

How an alloreactive T-cell receptor achieves peptide and MHC specificity

scientific article published on June 2017

How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

scientific article

Identification and engineering of human variable regions that allow expression of stable single-chain T cell receptors.

scientific article

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design

scientific article published on 14 December 2018

Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design

scientific article

Increased peptide contacts govern high affinity binding of a modified TCR whilst maintaining a native pMHC docking mode

scientific article

Interactions between CLIP-170, tubulin, and microtubules: implications for the mechanism of Clip-170 plus-end tracking behavior.

scientific article

Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship

scientific article published on 23 April 2008

LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain

scientific article published on 25 September 2019

Ligand-Driven T Cell Receptor Selection in Celiac Disease

scientific article published in October 2016

Limitations of time-resolved fluorescence suggested by molecular simulations: assessing the dynamics of T cell receptor binding loops.

scientific article

Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: IMPLICATIONS FOR VACCINE DESIGN

scientific article

Lysine Nζ-Decarboxylation Switch and Activation of the β-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus ⬇️

scientific article published on July 20, 2011

MHC Bias by T Cell Receptors: Genetic Evidence for MHC and TCR Coevolution.

scientific article published on 8 December 2016

MHC allele-specific molecular features determine peptide/HLA-A2 conformations that are recognized by HLA-A2-restricted T cell receptors

scientific article published on September 2002

Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection

scientific article published on 20 June 2019

Methods for Quantifying T cell Receptor Binding Affinities and Thermodynamics ⬇️

scientific article published on November 13, 2009

Modeling Sequence-Dependent Peptide Fluctuations in Immunologic Recognition.

scientific article published on 11 July 2017

Molecular properties of gp100-reactive T-cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells

scientific article published on 13 August 2018

Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings

scientific article

Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition.

scientific article

Plasticity in the contribution of T cell receptor variable region residues to binding of peptide-HLA-A2 complexes

scientific article

Poor immunogenicity of a self/tumor antigen derives from peptide-MHC-I instability and is independent of tolerance

scientific article published on August 2004

Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope

scientific article published on 05 November 2021

Strategic mutations in the class I major histocompatibility complex HLA-A2 independently affect both peptide binding and T cell receptor recognition

scientific article

Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism

scientific article

Structural dissimilarity from self drives neoepitope escape from immune tolerance

scientific article published on 17 August 2020

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

scientific article

Structure Based Prediction of Neoantigen Immunogenicity

scientific article published on 28 August 2019

Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition

scientific article

Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A0201: Implications for WT1-based cancer therapeutics

scientific article

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

scientific article

T cell receptor binding transition states and recognition of peptide/MHC.

scientific article published on 24 January 2007

T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability.

scientific article published on 17 September 2018

T cell receptor recognition via cooperative conformational plasticity.

scientific article published on 22 August 2006

T-cell Receptor Specificity Maintained by Altered Thermodynamics

scientific article

T-cell Receptor-optimized Peptide Skewing of the T-cell Repertoire Can Enhance Antigen Targeting

scientific article

TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility

scientific article published on 12 February 2014

TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms ⬇️

scientific article published on July 27, 2011

The basis for limited specificity and MHC restriction in a T cell receptor interface

scientific article

The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics

scientific article published on 01 December 2018

Thermodynamic and Kinetic Analysis of a Peptide−Class I MHC Interaction Highlights the Noncovalent Nature and Conformational Dynamics of the Class I Heterotrimer ⬇️

scientific article published on May 6, 2003

Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities

scientific article published on July 2008

Two different T cell receptors use different thermodynamic strategies to recognize the same peptide/MHC ligand

scientific article published on 05 January 2005

Understanding TCR affinity, antigen specificity, and cross-reactivity to improve TCR gene-modified T cells for cancer immunotherapy

scientific article published on 08 October 2019

Unraveling a hotspot for TCR recognition on HLA-A2: evidence against the existence of peptide-independent TCR binding determinants

scientific article

Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands

scientific article published on 31 January 2017

List of works by Brian M. Baker

2064: Deconstructing the peptide specificity of TCR recognition

3348 Structural Determinants of Neoantigen Immunogenicity for Cancer Therapy

4322 Structure-guided design of the TIL1383I T cell receptor

A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves

A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.

Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells

An Amino Acid Position at Crossroads of Evolution of Protein Function: ANTIBIOTIC SENSOR DOMAIN OF BlaR1 PROTEIN FROM STAPHYLOCOCCUS AUREUS VERSUS CLASS D -LACTAMASES

An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.

An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes

An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection

Changing the peptide specificity of a human T-cell receptor by directed evolution.

Citizens unite for computational immunology!

Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

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

Computational Modeling of T Cell Receptor Complexes

Computational Reprogramming of T Cell Antigen Receptor Binding Properties

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

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

Correction to: Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells.

Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells

Crystal Structures of HLA-A*0201 Complexed with Melan-A/MART-1 26(27L)-35 Peptidomimetics Reveal Conformational Heterogeneity and Highlight Degeneracy of T Cell Recognition

Cutting edge: Evidence for a dynamically driven T cell signaling mechanism.

Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex

Design, synthesis and evaluation of β-lactam antigenic peptide hybrids; unusual opening of the β-lactam ring in acidic media ⬇️

Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes

Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity

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

Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes

Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity

FOXO3-NF-κB RelA Protein Complexes Reduce Proinflammatory Cell Signaling and Function

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

Full-length influenza hemagglutinin HA2 refolds into the trimeric low-pH-induced conformation

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen

Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides

How an alloreactive T-cell receptor achieves peptide and MHC specificity

How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

Identification and engineering of human variable regions that allow expression of stable single-chain T cell receptors.

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design

Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design

Increased peptide contacts govern high affinity binding of a modified TCR whilst maintaining a native pMHC docking mode

Interactions between CLIP-170, tubulin, and microtubules: implications for the mechanism of Clip-170 plus-end tracking behavior.

Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship

LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain

Ligand-Driven T Cell Receptor Selection in Celiac Disease

Limitations of time-resolved fluorescence suggested by molecular simulations: assessing the dynamics of T cell receptor binding loops.

Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: IMPLICATIONS FOR VACCINE DESIGN

Lysine Nζ-Decarboxylation Switch and Activation of the β-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus ⬇️

MHC Bias by T Cell Receptors: Genetic Evidence for MHC and TCR Coevolution.

MHC allele-specific molecular features determine peptide/HLA-A2 conformations that are recognized by HLA-A2-restricted T cell receptors

Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection

Methods for Quantifying T cell Receptor Binding Affinities and Thermodynamics ⬇️

Modeling Sequence-Dependent Peptide Fluctuations in Immunologic Recognition.

Molecular properties of gp100-reactive T-cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells

Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings

Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition.

Plasticity in the contribution of T cell receptor variable region residues to binding of peptide-HLA-A2 complexes

Poor immunogenicity of a self/tumor antigen derives from peptide-MHC-I instability and is independent of tolerance

Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope

Strategic mutations in the class I major histocompatibility complex HLA-A2 independently affect both peptide binding and T cell receptor recognition

Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism

Structural dissimilarity from self drives neoepitope escape from immune tolerance

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

Structure Based Prediction of Neoantigen Immunogenicity

Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition

Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A0201: Implications for WT1-based cancer therapeutics

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

T cell receptor binding transition states and recognition of peptide/MHC.

T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability.

T cell receptor recognition via cooperative conformational plasticity.

T-cell Receptor Specificity Maintained by Altered Thermodynamics

T-cell Receptor-optimized Peptide Skewing of the T-cell Repertoire Can Enhance Antigen Targeting

TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility

TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms ⬇️

The basis for limited specificity and MHC restriction in a T cell receptor interface

The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics