Institute collection and analysis of Nanobodies (iCAN): a comprehensive database and analysis platform for nanobodies

Abstract

BackgroundNanobodies are single-domain antibodies that contain the unique structural and functional properties of naturally-occurring heavy chain in camelidae. As a novel class of antibody, they show many advantages compared with traditional antibodies such as smaller size, higher stability, improved specificity, more easily expressed in microorganisms. These unusual hallmarks make them as promising tools in basic research and clinical practice. Although thousands of nanobodies are known to be published, no single database provides searchable, unified annotation and integrative analysis tools for these various nanobodies.ResultsHere, we present the database of Institute Collection and Analysis of Nanobodies (iCAN). It is built for the aim that addressing the above gap to expand and accelerate the nanobody research. iCAN, as the first database of nanobody, contains the most comprehensive information to date on nanobodies and related antigens. So far, iCAN incorporates 2391 entries which include 2131 from patents and 260 from publications and provides a simple user interface for researchers to retrieve and view the detailed information of nanobodies. In addition to the data collection, iCAN also provides online bioinformatic tools for sequence analysis and characteristic feature extraction.ConclusionsIn summary, iCAN enables researchers to analyze nanobody features and explore the applications of nanobodies more efficiently. iCAN is freely available at http://ican.ils.seu.edu.cn.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4204-6) contains supplementary material, which is available to authorized users.

Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

“…In their 2017 study, Zuo and co-workers (Zuo et al, 2017) found more than 2,300 sequences of V H H domains, but 90% in patents and only 74% in PDB structures. With the availability of huge numbers of V H H sequences in the large majority of the proteins, it is interesting and essential to predict models of V H H domains, to understand their binding and specific properties.…”

A small protein probe for correlated microscopy of endogenous proteins

“…As nanobodies are single-chain-binding units, small, and to be generated against any possible target, the nanobody is currently the preferred binding unit. Moreover, given the versatility of nanobody applications (Beghein and Gettemans 2017 ) and recent establishment of a centralized nanobody database collection (ICAN; Zuo et al 2017 ), the expansion of the FLIPPER-bodies has great promise. However, alternative small, single-domain-binding scaffolds capable of binding with high affinity to their target such as affibodies may also be employed in the FLIPPER-body technology (Helma et al 2015 ).…”

Generation, expression and utilization of single-domain antibodies for in vivo protein localization and manipulation in sea urchin embryos

“…Validated nanobody sequences can be found in publicly available protein or Nb-specific databases (Zuo et al, 2017), shared upon request from lab groups, or can be purchased as plasmids from Addgene or individual companies (Appendix). …”

“…iCAN (Institute Collection and Analysis of Nanobody): http://ican.ils.seu.edu.cn/Home/Index/can (Zuo et al, 2017) Over 100,000 freely accessible sequences as of August 2018Searchable though keywords (i.e., GFP, actin)Video tutorial for searching and adding to the databaseDownloadable search results include Available DNA and protein sequencesRelated publications (PubMed ID)Source organism and experimental methods of screeningFunction (i.e., crystallization or imaging)Patent information…”