Literature DB >> 30441908

sdAb-DB: The Single Domain Antibody Database.

Emily E Wilton1, Michael P Opyr2, Senthilkumar Kailasam1, Ronja F Kothe1, Hans-Joachim Wieden1.   

Abstract

The Single Domain Antibody Database, or sdAb-DB, ( www.sdab-db.ca ) is the first freely available repository for single domain antibodies and related classes of proteins. Due to their small size, modular structure, and ease of expression, single domain antibodies (sdAb) have a wide range of applications, including as a rational design tool, and are therefore of great interest for synthetic biologists and bioengineers. However, to enable effective use and sharing of existing sdAbs, including those with engineered functions ( e.g., fusions with fluorescent proteins), as well as the rational design and engineering of new sdAbs, it is necessary to have access to sequences and experimental data. We have therefore developed a publicly available, sdAb-focused database, providing access to manually curated sdAb data from protein databases, published scientific articles, and user submissions. The sdAb-DB is an open-source repository and sharing platform for the sdAb community, providing access to performance data and basic bioinformatic tools for use with previously described and validated sdAbs, as well as for the engineering of new sdAb-based designs and proteins.

Entities:  

Keywords:  bioengineering; database; nanobody; open-source; single domain antibody (sdAb); synthetic biology

Mesh:

Substances:

Year:  2018        PMID: 30441908     DOI: 10.1021/acssynbio.8b00407

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN: 2161-5063            Impact factor:   5.110


  19 in total

1.  Chemogenetic Control of Nanobodies.

Authors:  Helen Farrants; Miroslaw Tarnawski; Thorsten G Müller; Shotaro Otsuka; Julien Hiblot; Birgit Koch; Moritz Kueblbeck; Hans-Georg Kräusslich; Jan Ellenberg; Kai Johnsson
Journal:  Nat Methods       Date:  2020-02-17       Impact factor: 28.547

Review 2.  Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies.

Authors:  Rahmad Akbar; Habib Bashour; Puneet Rawat; Philippe A Robert; Eva Smorodina; Tudor-Stefan Cotet; Karine Flem-Karlsen; Robert Frank; Brij Bhushan Mehta; Mai Ha Vu; Talip Zengin; Jose Gutierrez-Marcos; Fridtjof Lund-Johansen; Jan Terje Andersen; Victor Greiff
Journal:  MAbs       Date:  2022 Jan-Dec       Impact factor: 5.857

Review 3.  A guide to the optogenetic regulation of endogenous molecules.

Authors:  Kyrylo Yu Manoilov; Vladislav V Verkhusha; Daria M Shcherbakova
Journal:  Nat Methods       Date:  2021-08-26       Impact factor: 28.547

4.  Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies.

Authors:  Olena S Oliinyk; Mikhail Baloban; Charles L Clark; Erin Carey; Sergei Pletnev; Axel Nimmerjahn; Vladislav V Verkhusha
Journal:  Nat Methods       Date:  2022-05-23       Impact factor: 47.990

5.  ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity.

Authors:  Aysima Hacisuleyman; Burak Erman
Journal:  J Biol Phys       Date:  2020-05-16       Impact factor: 1.365

Review 6.  Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics.

Authors:  Rahul Khetan; Robin Curtis; Charlotte M Deane; Johannes Thorling Hadsund; Uddipan Kar; Konrad Krawczyk; Daisuke Kuroda; Sarah A Robinson; Pietro Sormanni; Kouhei Tsumoto; Jim Warwicker; Andrew C R Martin
Journal:  MAbs       Date:  2022 Jan-Dec       Impact factor: 5.857

Review 7.  Strategies and Tactics for the Development of Selective Glycan-Binding Proteins.

Authors:  Elizabeth M Ward; Megan E Kizer; Barbara Imperiali
Journal:  ACS Chem Biol       Date:  2021-01-26       Impact factor: 4.634

8.  Antibody RING-Mediated Destruction of Endogenous Proteins.

Authors:  Adel F M Ibrahim; Linnan Shen; Michael H Tatham; David Dickerson; Alan R Prescott; Naima Abidi; Dimitris P Xirodimas; Ronald T Hay
Journal:  Mol Cell       Date:  2020-05-25       Impact factor: 17.970

9.  Optogenetic regulation of endogenous proteins.

Authors:  Taras A Redchuk; Maksim M Karasev; Polina V Verkhusha; Sara K Donnelly; Maren Hülsemann; Jori Virtanen; Henna M Moore; Maria K Vartiainen; Louis Hodgson; Vladislav V Verkhusha
Journal:  Nat Commun       Date:  2020-01-30       Impact factor: 14.919

10.  Computational approaches to therapeutic antibody design: established methods and emerging trends.

Authors:  Richard A Norman; Francesco Ambrosetti; Alexandre M J J Bonvin; Lucy J Colwell; Sebastian Kelm; Sandeep Kumar; Konrad Krawczyk
Journal:  Brief Bioinform       Date:  2020-09-25       Impact factor: 11.622

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