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

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

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

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

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

(2012) G. T. Kapp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

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

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

Computational Design of the Sequence and Structure of a Protein-Binding Peptide

(2011) Deanne W. Sammond et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

(2011) Bryan S. Der et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

A Generic Program for Multistate Protein Design

(2011) Andrew Leaver-Fay et al.   PLoS One

Computational design of a symmetric homodimer using  -strand assembly

(2011) P. B. Stranges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restricted sidechain plasticity in the structures of native proteins and complexes

(2011) Sarel J. Fleishman et al.   PROTEIN SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Computational Design of a PAK1 Binding Protein

(2010) Ramesh K. Jha et al.   JOURNAL OF MOLECULAR BIOLOGY

What Makes Ras an Efficient Molecular Switch: A Computational, Biophysical, and Structural Study of Ras-GDP Interactions with Mutants of Raf

(2010) Daniel Filchtinski et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational design of affinity and specificity at protein–protein interfaces

(2009) John Karanicolas et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Probability Distributions of Hydration Water Molecules around Polar Protein Atoms Obtained by a Database Analysis

(2009) Daisuke Matsuoka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

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

(2009) Daniel J Mandell et al.   NATURE METHODS

Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

(2008) Kimberly A. Reynolds et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Redesign of a Protein–Protein Interface for High Affinity and Binding Specificity Using Modular Architecture and Naturally Occurring Template Fragments

(2008) V. Potapov et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity

(2008) Eliyahu Yosef et al.   JOURNAL OF MOLECULAR BIOLOGY

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

(2008) Xiaozhen Hu et al.   STRUCTURE