Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies

Coronavirus Infections—More Than Just the Common Cold

(2020) Catharine I. Paules et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

(2020) Davide F. Robbiani et al.   NATURE

Neutralizing antibodies for the treatment of COVID-19

(2020) Shibo Jiang et al.   Nature Biomedical Engineering

Engineered peptide barcodes for in-depth analyses of binding protein libraries

(2019) Pascal Egloff et al.   NATURE METHODS

Principles for Integrative Structural Biology Studies

(2019) Michael P. Rout et al.   CELL

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

(2019) Zhen-Lin Chen et al.   Nature Communications

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Principles for computational design of binding antibodies

(2017) Dror Baran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

(2016) Honglan Li et al.   BMC GENOMICS

Revealing Higher Order Protein Structure Using Mass Spectrometry

(2016) Brian T. Chait et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Improving Loop Modeling of the Antibody Complementarity-Determining Region 3 Using Knowledge-Based Restraints

(2016) Jessica A. Finn et al.   PLoS One

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

(2016) Alexander Leitner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Immuno-targeting the multifunctional CD38 using nanobody

(2016) Ting Li et al.   Scientific Reports

Germinal Center Selection and the Antibody Response to Influenza

(2015) Gabriel D. Victora et al.   CELL

Viral Receptor-Binding Site Antibodies with Diverse Germline Origins

(2015) Aaron G. Schmidt et al.   CELL

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis

(2014) Johannes Trück et al.   JOURNAL OF IMMUNOLOGY

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

(2014) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

A robust pipeline for rapid production of versatile nanobody repertoires

(2014) Peter C Fridy et al.   NATURE METHODS

Origins of specificity and affinity in antibody–protein interactions

(2014) Hung-Pin Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanobodies: Natural Single-Domain Antibodies

(2013) Serge Muyldermans   Annual Review of Biochemistry

Optimized atomic statistical potentials: assessment of protein interfaces and loops

(2013) Guang Qiang Dong et al.   BIOINFORMATICS

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response

(2013) Y. Wine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structural Basis of Antibody-Antigen Recognition

(2013) Inbal Sela-Culang et al.   Frontiers in Immunology

A method for integrative structure determination of protein-protein complexes

(2012) Dina Schneidman-Duhovny et al.   BIOINFORMATICS

Immunodominance: A pivotal principle in host response to viral infections

(2012) Ali Akram et al.   CLINICAL IMMUNOLOGY

Proteomics-directed cloning of circulating antiviral human monoclonal antibodies

(2012) Shuji Sato et al.   NATURE BIOTECHNOLOGY

Human viruses: discovery and emergence

(2012) M. Woolhouse et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Analysis and Modeling of the Variable Region of Camelid Single-Domain Antibodies

(2011) A. Sircar et al.   JOURNAL OF IMMUNOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

(2011) J. F. Scheid et al.   SCIENCE

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus

(2008) Anita Y. Lam et al.   JOURNAL OF STRUCTURAL BIOLOGY

Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains

(2008) K.R. Abhinandan et al.   MOLECULAR IMMUNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Does Trypsin Cut Before Proline?

(2007) Jesse Rodriguez et al.   JOURNAL OF PROTEOME RESEARCH