| Contents |
Computational design of novel protein binders and experimental affinity maturation / Timothy A. Whitehead, David Baker, and Sarel J. Fleishman -- Mining tertiary structural motifs for assessment of designability / Jian Zhang and Gevorg Grigoryan -- Computational methods for controlling binding specificity / Oz Sharabi, Ariel Erijman, and Julia M. Shifman -- Flexible backbone sampling methods to model and design protein alternative conformations / Noah Ollikainen, Colin A. Smith, James S. Fraser, and Tanja Kortemme -- Osprey : protein design with ensembles, flexibility, and provable algorithms / Pablo Gainza, Kyle E. Roberts, Ivelin Georgiev, Ryan H. Lilien, Daniel A. Keedy, Cheng-Yu Chen, Faisal Reza, Amy C. Anderson, David C. Richardson, Jane S. Richardson, and Bruce R. Donald -- Scientific benchmarks for guiding macromolecular energy function improvement / Andrew Leaver-Fay, Matthew J. O'Meara, Mike Tyka, Ron Jacak, Yifan Song, Elizabeth H. Kellogg, James Thompson, Ian W. Davis, Roland A. Pache, Sergey Lyskov, Jeffrey J. Gray, Tanja Kortemme, Jane S. Richardson, James J. Havranek, Jack Snoeyink, David Baker, and Brian Kuhlman -- Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins / Gert Kiss, Vijay S. Pande, and K.N. Houk -- Multistate protein design using CLEVER and CLASSY / Christopher Negron and Amy E. Keating -- Using analyses of amino acid coevolution to understand protein structure and function / Orr Ashenberg and Michael T. Laub -- Evolution-based design of proteins / Kimberly A. Reynolds, William P. Russ, Michael Socolich, and Rama Ranganathan -- Protein engineering and stabilization from sequence statistics : variation and covariation analysis / Venuka Durani and Thomas J. Magliery -- Enzyme engineering by targeted libraries / Moshe Goldsmith and Dan S. Tawfik -- Generation of high-performance binding proteins for pepetide motifs by affinity clamping / Shohei Koide and Jin Huang -- Engineering fibronectin-based binding proteins by yeast surface display / Tiffany F. Chen, Seymour de Picciotto, Benjamin J. Hackel, and K. Dane Wittrup -- Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing / Megan E. McLaughlin and Sachdev S. Sidhu -- Efficient sampling of SCHEMA chimera families to identify useful sequence elements / Pete Heinzelman, Philip A. Romero, and Frances H. Arnold -- Protein switch engineering by domain insertion / Manu Kanwar, R. Clay Wright, Amol Date, Jennifer Tullman, and Marc Ostermeier -- Design of chimeric proteins by combination of subdomain-sized fragments / José Arcadio Farías Rico, and Birte Höcker-- [alpha]-helix mimicry with [alpha/beta]-peptides / Lisa M. Johnson and Samuel H. Gellman. |
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