List of works - Brian G Pierce

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

scientific article published on January 2013

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

Accelerating protein docking in ZDOCK using an advanced 3D convolution library ⬇️

scientific article

Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice.

scientific article

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

scientific article published on 03 February 2021

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking

scientific article published on 08 February 2022

Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design

scientific article published on 02 February 2021

Antigenicity and Immunogenicity of Differentially Glycosylated Hepatitis C Virus E2 Envelope Proteins Expressed in Mammalian and Insect Cells

scientific article published on 21 March 2019

Backbone flexibility of CDR3 and immune recognition of antigens

scientific article published on 28 December 2013

Benchmarking <scp>AlphaFold</scp> for protein complex modeling reveals accuracy determinants

scientific article published in 2022

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis C virus infections uncover molecular determinants for E2 targeting and vaccine design

scientific article published on 17 May 2019

Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas

scientific article published on 14 April 2020

Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains.

scientific article

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

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

scientific article

Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition.

scientific article published on 28 May 2018

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

Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies

scientific article

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

scientific article

Designing a B Cell-Based Vaccine against a Highly Variable Hepatitis C Virus

scientific article published in January 2017

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

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

Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design

scientific article published on 26 October 2016

Hepatitis C virus vaccine candidates inducing protective neutralizing antibodies

scientific article

High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody

scientific article

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

scientific article

Integrating statistical pair potentials into protein complex prediction

scientific article published in November 2007

M-ZDOCK: a grid-based approach for Cn symmetric multimer docking

scientific article published on 21 December 2004

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Mapping Determinants of Virus Neutralization and Viral Escape for Rational Design of a Hepatitis C Virus Vaccine.

scientific article published on 31 May 2018

Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein–Protein Interaction

scientific article

Newcastle disease virus vectors expressing consensus sequence of the H7 HA protein protect broiler chickens and turkeys against highly pathogenic H7N8 virus

scientific article published on 15 July 2019

Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites

scientific article published in Journal of Biological Chemistry

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

scientific article published on 7 October 2016

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

scientific article published on November 2010

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Prediction of protein–protein binding free energies ⬇️

scientific article published on February 2, 2012

Protein-protein docking: overview and performance analysis.

scientific article published on January 2008

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

scientific article published on September 2012

Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope

scientific article

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants

scientific article published on 07 September 2021

Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors

scientific article published on 10 January 2022

Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen

scientific article published on 09 June 2020

Structural basis for penetration of the glycan shield of hepatitis C virus E2 glycoprotein by a broadly neutralizing human antibody

scientific article

Structure-Based Design of Hepatitis C Virus Vaccines that Elicit Neutralizing Antibody Responses to a Conserved Epitope

scientific article published on 9 August 2017

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

scientific article

TCR3d: The T cell receptor structural repertoire database

scientific article published on 01 December 2019

TCRmodel: high resolution modeling of T cell receptors from sequence.

scientific article published in July 2018

The Missing Heritability in T1D and Potential New Targets for Prevention.

scientific article published on 13 March 2013

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

scientific article published in December 2007

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

scientific article

Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic

scientific article

Viral evasion and challenges of hepatitis C virus vaccine development

scientific article published on 19 September 2016

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

scientific article published on 01 August 2005

ZRANK: reranking protein docking predictions with an optimized energy function

scientific article published in June 2007

Zika virus NS5 protein antagonizes type I interferon production via blocking TBK1 activation

article

List of works by Brian G Pierce

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

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.

Accelerating protein docking in ZDOCK using an advanced 3D convolution library ⬇️

Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice.

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking

Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design

Antigenicity and Immunogenicity of Differentially Glycosylated Hepatitis C Virus E2 Envelope Proteins Expressed in Mammalian and Insect Cells

Backbone flexibility of CDR3 and immune recognition of antigens

Benchmarking <scp>AlphaFold</scp> for protein complex modeling reveals accuracy determinants

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis C virus infections uncover molecular determinants for E2 targeting and vaccine design

Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas

Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

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

Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition.

Computational Modeling of T Cell Receptor Complexes

Computational Reprogramming of T Cell Antigen Receptor Binding Properties

Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies

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

Designing a B Cell-Based Vaccine against a Highly Variable Hepatitis C Virus

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

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

Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design

Hepatitis C virus vaccine candidates inducing protective neutralizing antibodies

High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody

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

Integrating statistical pair potentials into protein complex prediction

M-ZDOCK: a grid-based approach for Cn symmetric multimer docking

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Mapping Determinants of Virus Neutralization and Viral Escape for Rational Design of a Hepatitis C Virus Vaccine.

Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein–Protein Interaction

Newcastle disease virus vectors expressing consensus sequence of the H7 HA protein protect broiler chickens and turkeys against highly pathogenic H7N8 virus

Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Prediction of protein–protein binding free energies ⬇️

Protein-protein docking: overview and performance analysis.

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope

Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants

Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors

Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen

Structural basis for penetration of the glycan shield of hepatitis C virus E2 glycoprotein by a broadly neutralizing human antibody

Structure-Based Design of Hepatitis C Virus Vaccines that Elicit Neutralizing Antibody Responses to a Conserved Epitope

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

TCR3d: The T cell receptor structural repertoire database

TCRmodel: high resolution modeling of T cell receptors from sequence.

The Missing Heritability in T1D and Potential New Targets for Prevention.

The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic

Viral evasion and challenges of hepatitis C virus vaccine development

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

ZRANK: reranking protein docking predictions with an optimized energy function

Zika virus NS5 protein antagonizes type I interferon production via blocking TBK1 activation