A critical analysis of computational protein design with sparse residue interaction graphs

Algorithms for protein design

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

BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design

(2016) Jonathan D. Jou et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Computational Protein Design Using AND/OR Branch-and-Bound Search

(2016) Yichao Zhou et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design

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

Computational design and experimental verification of a symmetric protein homodimer

(2015) Yun Mou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Removing T-cell epitopes with computational protein design

(2014) C. King et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Iterative approach to computational enzyme design

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

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

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

De novo protein design using pairwise potentials and a genetic algorithm

(2010) David T. Jones   PROTEIN SCIENCE

A new approach to the design of uniquely folded thermally stable proteins

(2010) Xin Jiang et al.   PROTEIN SCIENCE

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Algorithm for backrub motions in protein design

(2008) I. Georgiev et al.   BIOINFORMATICS

A computational framework to empower probabilistic protein design

(2008) M. Fromer 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

Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space

(2008) Menachem Fromer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS