Literature DB >> 23422423

Computational design of novel protein binders and experimental affinity maturation.

Timothy A Whitehead1, David Baker, Sarel J Fleishman.   

Abstract

Computational design of novel protein binders has recently emerged as a useful technique to study biomolecular recognition and generate molecules for use in biotechnology, research, and biomedicine. Current limitations in computational design methodology have led to the adoption of high-throughput screening and affinity maturation techniques to diagnose modeling inaccuracies and generate high activity binders. Here, we scrutinize this combination of computational and experimental aspects and propose areas for future methodological improvements.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23422423     DOI: 10.1016/B978-0-12-394292-0.00001-1

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  17 in total

1.  Computational design and experimental verification of a symmetric protein homodimer.

Authors:  Yun Mou; Po-Ssu Huang; Fang-Ciao Hsu; Shing-Jong Huang; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-12       Impact factor: 11.205

Review 2.  Protein modeling: what happened to the "protein structure gap"?

Authors:  Torsten Schwede
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

Review 3.  Using anchoring motifs for the computational design of protein-protein interactions.

Authors:  Timothy M Jacobs; Brian Kuhlman
Journal:  Biochem Soc Trans       Date:  2013-10       Impact factor: 5.407

Review 4.  Engineering CAR-T cells: Design concepts.

Authors:  Shivani Srivastava; Stanley R Riddell
Journal:  Trends Immunol       Date:  2015-07-11       Impact factor: 16.687

Review 5.  Design and implementation of adoptive therapy with chimeric antigen receptor-modified T cells.

Authors:  Michael C Jensen; Stanley R Riddell
Journal:  Immunol Rev       Date:  2014-01       Impact factor: 12.988

Review 6.  Recent advances in automated protein design and its future challenges.

Authors:  Dani Setiawan; Jeffrey Brender; Yang Zhang
Journal:  Expert Opin Drug Discov       Date:  2018-04-25       Impact factor: 6.098

Review 7.  Practically useful protein-design methods combining phylogenetic and atomistic calculations.

Authors:  Jonathan Weinstein; Olga Khersonsky; Sarel J Fleishman
Journal:  Curr Opin Struct Biol       Date:  2020-06-05       Impact factor: 6.809

8.  Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Authors:  Marc F Lensink; Guillaume Brysbaert; Nurul Nadzirin; Sameer Velankar; Raphaël A G Chaleil; Tereza Gerguri; Paul A Bates; Elodie Laine; Alessandra Carbone; Sergei Grudinin; Ren Kong; Ran-Ran Liu; Xi-Ming Xu; Hang Shi; Shan Chang; Miriam Eisenstein; Agnieszka Karczynska; Cezary Czaplewski; Emilia Lubecka; Agnieszka Lipska; Paweł Krupa; Magdalena Mozolewska; Łukasz Golon; Sergey Samsonov; Adam Liwo; Silvia Crivelli; Guillaume Pagès; Mikhail Karasikov; Maria Kadukova; Yumeng Yan; Sheng-You Huang; Mireia Rosell; Luis A Rodríguez-Lumbreras; Miguel Romero-Durana; Lucía Díaz-Bueno; Juan Fernandez-Recio; Charles Christoffer; Genki Terashi; Woong-Hee Shin; Tunde Aderinwale; Sai Raghavendra Maddhuri Venkata Subraman; Daisuke Kihara; Dima Kozakov; Sandor Vajda; Kathryn Porter; Dzmitry Padhorny; Israel Desta; Dmitri Beglov; Mikhail Ignatov; Sergey Kotelnikov; Iain H Moal; David W Ritchie; Isaure Chauvot de Beauchêne; Bernard Maigret; Marie-Dominique Devignes; Maria E Ruiz Echartea; Didier Barradas-Bautista; Zhen Cao; Luigi Cavallo; Romina Oliva; Yue Cao; Yang Shen; Minkyung Baek; Taeyong Park; Hyeonuk Woo; Chaok Seok; Merav Braitbard; Lirane Bitton; Dina Scheidman-Duhovny; Justas Dapkūnas; Kliment Olechnovič; Česlovas Venclovas; Petras J Kundrotas; Saveliy Belkin; Devlina Chakravarty; Varsha D Badal; Ilya A Vakser; Thom Vreven; Sweta Vangaveti; Tyler Borrman; Zhiping Weng; Johnathan D Guest; Ragul Gowthaman; Brian G Pierce; Xianjin Xu; Rui Duan; Liming Qiu; Jie Hou; Benjamin Ryan Merideth; Zhiwei Ma; Jianlin Cheng; Xiaoqin Zou; Panagiotis I Koukos; Jorge Roel-Touris; Francesco Ambrosetti; Cunliang Geng; Jörg Schaarschmidt; Mikael E Trellet; Adrien S J Melquiond; Li Xue; Brian Jiménez-García; Charlotte W van Noort; Rodrigo V Honorato; Alexandre M J J Bonvin; Shoshana J Wodak
Journal:  Proteins       Date:  2019-10-25

Review 9.  Data-driven computational protein design.

Authors:  Vincent Frappier; Amy E Keating
Journal:  Curr Opin Struct Biol       Date:  2021-04-25       Impact factor: 7.786

10.  Design of a basigin-mimicking inhibitor targeting the malaria invasion protein RH5.

Authors:  Shira Warszawski; Elya Dekel; Ivan Campeotto; Jennifer M Marshall; Katherine E Wright; Oliver Lyth; Orli Knop; Neta Regev-Rudzki; Matthew K Higgins; Simon J Draper; Jake Baum; Sarel J Fleishman
Journal:  Proteins       Date:  2019-08-02
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