A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments

OPTIMIZATION OF THERAPEUTIC PROTEINS TO DELETE T-CELL EPITOPES WHILE MAINTAINING BENEFICIAL RESIDUE INTERACTIONS

(2011) ANDREW S. PARKER et al.   Journal of Bioinformatics and Computational Biology

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence

(2010) Xiaojian Shao et al.   BIOINFORMATICS

Optimization algorithms for functional deimmunization of therapeutic proteins

(2010) Andrew S Parker et al.   BMC BIOINFORMATICS

Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination

(2010) Pete Heinzelman et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

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

Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics

(2009) Anne S. De Groot et al.   CLINICAL IMMUNOLOGY

Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins

(2009) Wei Zheng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2009) Gevorg Grigoryan et al.   NATURE

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

A family of thermostable fungal cellulases created by structure-guided recombination

(2009) P. Heinzelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Graphical models of protein-protein interaction specificity from correlated mutations and interaction data

(2009) John Thomas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolutionary Pareto-optimization of stably folding peptides

(2008) Wolfram Gronwald et al.   BMC BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation

(2008) Hetunandan Kamisetty et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Pareto optimization in computational protein design with multiple objectives

(2008) María Suárez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach

(2008) Peng Wang et al.   PLoS Computational Biology