Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface

Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane

(2018) Bindu Lakshman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

OSPREY 3.0: Open-source protein redesign for you, with powerful new features

(2018) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Algorithms for protein design

(2016) Pablo Gainza et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

comets(Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence

(2016) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast search algorithms for computational protein design

(2016) Seydou Traoré et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery

(2016) Roman Sommer et al.   Chemical Science

Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design

(2015) Mark A. Hallen et al.   Journal of Chemical Theory and Computation

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

(2015) David Simoncini et al.   Journal of Chemical Theory and Computation

Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations

(2015) J. C. Hunter et al.   MOLECULAR CANCER RESEARCH

Fast gap-free enumeration of conformations and sequences for protein design

(2015) Kyle E. Roberts et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Protein design algorithms predict viable resistance to an experimental antifolate

(2015) Stephanie M. Reeve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibodies VRC01 and 10E8 Neutralize HIV-1 with High Breadth and Potency Even with Ig-Framework Regions Substantially Reverted to Germline

(2014) I. S. Georgiev et al.   JOURNAL OF IMMUNOLOGY

Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo

(2014) R. S. Rudicell et al.   JOURNAL OF VIROLOGY

Off-rate screening for selection of high-affinity anti-drug antibodies

(2013) Francisco Ylera et al.   ANALYTICAL BIOCHEMISTRY

A new framework for computational protein design through cost function network optimization

(2013) Seydou Traoré et al.   BIOINFORMATICS

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration

(2013) Nathaniel W. Silver et al.   Journal of Chemical Theory and Computation

Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility

(2013) Mark A. Hallen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-Mediated Activation

(2012) Qi Sun et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

Design of epitope-specific probes for sera analysis and antibody isolation

(2012) I Georgiev et al.   Retrovirology

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

(2012) Kyle E. Roberts et al.   PLoS Computational Biology

Protein Design Using Continuous Rotamers

(2012) Pablo Gainza et al.   PLoS Computational 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

Predicting resistance mutations using protein design algorithms

(2010) K. M. Frey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Binding of Raf to Ras·GDP Is Correlated with Biological Activity

(2009) Christina Kiel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Computational structure-based redesign of enzyme activity

(2009) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algorithm for backrub motions in protein design

(2008) I. Georgiev et al.   BIOINFORMATICS

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

(2008) Ivelin Georgiev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computational protein design with side-chain conformational entropy

(2008) Daniele Sciretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS