Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces

Principles of Protein Stability and Their Application in Computational Design

(2018) Adi Goldenzweig et al.   Annual Review of Biochemistry

Highly active enzymes by automated combinatorial backbone assembly and sequence design

(2018) Gideon Lapidoth et al.   Nature Communications

AbPredict 2: A server for accurate and unstrained structure prediction of antibody variable domains

(2018) Gideon Lapidoth et al.   BIOINFORMATICS

Automated Design of Efficient and Functionally Diverse Enzyme Repertoires

(2018) Olga Khersonsky et al.   MOLECULAR CELL

Ultrahigh specificity in a network of computationally designed protein-interaction pairs

(2018) Ravit Netzer et al.   Nature Communications

Biophysical properties of the clinical-stage antibody landscape

(2017) Tushar Jain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen

(2017) Ivan Campeotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

(2017) Patrick Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability

(2017) Mark C. Julian et al.   Scientific Reports

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21

(2016) Isabel Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Why reinvent the wheel? Building new proteins based on ready-made parts

(2016) Olga Khersonsky et al.   PROTEIN SCIENCE

High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments

(2016) Christoffer H. Norn et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Inspired by nature

(2016) R. Netzer et al.   SCIENCE

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

(2016) S. E. Boyken et al.   SCIENCE

Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane

(2016) Assaf Elazar et al.   eLife

Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves

(2016) Rhys M Adams et al.   eLife

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

(2015) Matthew J. O’Meara et al.   Journal of Chemical Theory and Computation

Developability Assessment During the Selection of Novel Therapeutic Antibodies

(2015) Alexander Jarasch et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Boosting antibody developability through rational sequence optimization

(2015) Daniel Seeliger et al.   mAbs

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

(2015) Gideon D. Lapidoth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Disulfide bond generation in mammalian blood serum: detection and purification of quiescin-sulfhydryl oxidase

(2014) Benjamin A. Israel et al.   FREE RADICAL BIOLOGY AND MEDICINE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Second antibody modeling assessment (AMA-II)

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

An Inhibitory Antibody Blocks the First Step in the Dithiol/Disulfide Relay Mechanism of the Enzyme QSOX1

(2013) Iris Grossman et al.   JOURNAL OF MOLECULAR BIOLOGY

Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing

(2013) Charles M. Forsyth et al.   mAbs

Developability studies before initiation of process development

(2013) Xiaoyu Yang et al.   mAbs

Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning

(2012) Yasuhiro Fujino et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies

(2012) Aleksandr E. Miklos et al.   CHEMISTRY & BIOLOGY

The dynamic disulphide relay of quiescin sulphydryl oxidase

(2012) Assaf Alon et al.   NATURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

General strategy for the generation of human antibody variable domains with increased aggregation resistance

(2012) K. Dudgeon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated selection of stabilizing mutations in designed and natural proteins

(2012) B. Borgo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The association of heavy and light chain variable domains in antibodies: implications for antigen specificity

(2011) Anna Chailyan et al.   FEBS Journal

High Affinity, Developability and Functional Size: The Holy Grail of Combinatorial Antibody Library Generation

(2011) Dirk Ponsel et al.   MOLECULES

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

(2011) Sarel J. Fleishman et al.   PLoS One

Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression

(2010) Tamar Unger et al.   JOURNAL OF STRUCTURAL BIOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Analysis and prediction of VH/VL packing in antibodies

(2010) K. R. Abhinandan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

(2009) Huanting Liu et al.   BMC BIOTECHNOLOGY

Loss of Nkx3.1 leads to the activation of discrete downstream target genes during prostate tumorigenesis

(2009) H Song et al.   ONCOGENE

Design of therapeutic proteins with enhanced stability

(2009) N. Chennamsetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developability assessment in pharmaceutical industry: An integrated group approach for selecting developable candidates

(2008) Vishal Saxena et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning

(2007) Thomas Tiller et al.   JOURNAL OF IMMUNOLOGICAL METHODS