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

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

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

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

Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance

(2012) Maloy Kumar Parai et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Rational and Computational Design of Stabilized Variants of Cyanovirin-N That Retain Affinity and Specificity for Glycan Ligands

(2011) Vadim Patsalo et al.   BIOCHEMISTRY

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

(2011) Mariana Babor et al.   PROTEIN SCIENCE

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Choreographing an enzyme's dance

(2010) Janice Villali et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Information-theoretic approaches to branching in search

(2010) Andrew Gilpin et al.   Discrete Optimization

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

Backbone flexibility in computational protein design

(2009) Daniel J Mandell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Rotamer optimization for protein design through MAP estimation and problem-size reduction

(2009) Eun-Jong Hong et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

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