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

The Role of Local Backrub Motions in Evolved and Designed Mutations

(2012) Daniel A. Keedy et al.   PLoS Computational Biology

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

Protein loop closure using orientational restraints from NMR data

(2011) Chittaranjan Tripathy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana 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

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions

(2010) Hetunandan Kamisetty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program

(2009) Vincent B. Chen et al.   PROTEIN SCIENCE

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

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

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology

The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state

(2008) Orna Almog et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An improved pairwise decomposable finite-difference Poisson–Boltzmann method for computational protein design

(2007) Christina L. Vizcarra et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY