Fast search algorithms for computational protein design

New emerging bio-catalysts design in biotransformations

(2015) Jose M. Palomo et al.   BIOTECHNOLOGY ADVANCES

Computational protein design as an optimization problem

(2014) David Allouche et al.   ARTIFICIAL INTELLIGENCE

Accurate design of co-assembling multi-component protein nanomaterials

(2014) Neil P. King et al.   NATURE

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

(2013) Seydou Traoré et al.   BIOINFORMATICS

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

Amino-acid site variability among natural and designed proteins

(2013) Eleisha L. Jackson et al.   PeerJ

Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies

(2012) Aleksandr E. Miklos et al.   CHEMISTRY & BIOLOGY

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

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Reasoning from last conflict(s) in constraint programming

(2009) Christophe Lecoutre et al.   ARTIFICIAL INTELLIGENCE

Computational design of affinity and specificity at protein–protein interfaces

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

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

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

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

Evaluating and optimizing computational protein design force fields using fixed composition-based negative design

(2008) O. Alvizo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA