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

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

(2016) Timothy P. Riley et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

(2016) Daniel T. Harris et al.   STRUCTURE

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

(2014) Sheena N. Smith et al.   Nature Communications

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

(2014) Brian G. Pierce et al.   PLoS Computational Biology

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

(2013) Zhixiu Li et al.   Annual Review of Biophysics

Enhanced-affinity murine T-cell receptors for tumor/self-antigens can be safe in gene therapy despite surpassing the threshold for thymic selection

(2013) T. M. Schmitt et al.   BLOOD

Computational design of protein–protein interactions

(2013) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Plasticity in the Contribution of T Cell Receptor Variable Region Residues to Binding of Peptide–HLA-A2 Complexes

(2013) Sheena N. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Design of a Protein-Based Enzyme Inhibitor

(2013) Erik Procko et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Directed evolution of proteins for increased stability and expression using yeast display

(2012) Michael W. Traxlmayr et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Construction of a Stability Landscape of the CH3 Domain of Human IgG1 by Combining Directed Evolution with High Throughput Sequencing

(2012) Michael W. Traxlmayr et al.   JOURNAL OF MOLECULAR BIOLOGY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

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

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

(2012) P. Benjamin Stranges et al.   PROTEIN SCIENCE

Interaction of Streptavidin-Based Peptide-MHC Oligomers (Tetramers) with Cell-Surface TCRs

(2011) J. D. Stone et al.   JOURNAL OF IMMUNOLOGY

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Four Small Puzzles That Rosetta Doesn't Solve

(2011) Rhiju Das   PLoS One

The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Practically Useful: What the RosettaProtein Modeling Suite Can Do for You

(2010) Kristian W. Kaufmann et al.   BIOCHEMISTRY

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

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

(2010) D. H. Aggen et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Stability engineering of scFvs for the development of bispecific and multivalent antibodies

(2010) Brian R. Miller 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

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

(2010) Ryan K. Shultzaberger et al.   PLoS Genetics

The Impact of TCR-Binding Properties and Antigen Presentation Format on T Cell Responsiveness

(2009) A. S. Chervin et al.   JOURNAL OF IMMUNOLOGY

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

(2009) Daniel J Mandell et al.   NATURE METHODS

The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains

(2009) Annemarie Honegger et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Engineering higher affinity T cell receptors using a T cell display system

(2008) Adam S. Chervin et al.   JOURNAL OF IMMUNOLOGICAL METHODS