SwiftLib: rapid degenerate-codon-library optimization through dynamic programming

Peptide Ligands for Pro-survival Protein Bfl-1 from Computationally Guided Library Screening

(2013) Sanjib Dutta et al.   ACS Chemical Biology

Optimal codon randomization via mathematical programming

(2013) Yuval Nov et al.   JOURNAL OF THEORETICAL BIOLOGY

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Structure-Based Redesign of the Binding Specificity of Anti-Apoptotic Bcl-xL

(2012) T. Scott Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reducing Codon Redundancy and Screening Effort of Combinatorial Protein Libraries Created by Saturation Mutagenesis

(2012) Sabrina Kille et al.   ACS Synthetic Biology

Optimization of Combinatorial Mutagenesis

(2011) Andrew S. Parker et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

(2011) M. L. Azoitei et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

(2010) Shaun M. Lippow et al.   CHEMISTRY & BIOLOGY

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

(2010) B. D. Allen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering a protein-protein interface using a computationally designed library

(2010) G. Guntas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries

(2010) R. A. Chica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial codons: A computer program to approximate amino acid probabilities with biased nucleotide usage

(2010) Ethan Wolf et al.   PROTEIN SCIENCE

Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series

(2009) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm

(2009) R. A. Craig et al.   NUCLEIC ACIDS RESEARCH

Macromolecular Modeling with Rosetta

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

Addressing the Numbers Problem in Directed Evolution

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions

(2008) Manfred T. Reetz et al.   CHEMICAL COMMUNICATIONS

Directed enzyme evolution via small and effective neutral drift libraries

(2008) Rinkoo D Gupta et al.   NATURE METHODS

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

(2008) A. E. Firth et al.   NUCLEIC ACIDS RESEARCH