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The ABCD database: a repository for chemically defined antibodies

2019 Nucleic Acids Research  
The ABCD (for AntiBodies Chemically Defined) database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases  ...  The ABCD database aims at helping to improve reproducibility in academic research by providing a unique, unambiguous identifier associated to each antibody sequence.  ...  OVERVIEW OF DATABASE CONTENT The ABCD database is, to our knowledge, the first effort to provide freely accessible, curated information on chemically defined antibodies (i.e. antibodies with a known primary  ... 
doi:10.1093/nar/gkz714 pmid:31410491 pmcid:PMC6943046 fatcat:ajdnpba2jnhcpl3h3rfblhk6zm

Increasing the use of animal-free recombinant antibodies

Katherine Groff
2020 ALTEX: Alternatives to Animal Experimentation  
Antibodies are used in a range of research, diagnostic, and regulatory applications.  ...  Traditional methods for producing such reagents involve the immunization of animals, which introduces variability into the methods that use them and is not aligned with efforts to replace and reduce animal  ...  Acknowledgements The meeting organizers thank the experts who attended the De- Katherine Groff 1 , David Allen 2 , Warren Casey 3 and Amy J. Clippinger 1  ... 
doi:10.14573/altex.2001071 pmid:31923318 fatcat:djf34jajxvaerchzrubfg6u7wi

ESC - a comprehensive resource for SARS-CoV-2 immune escape variants [article]

Mercy Rophina, Kavita Pandhare, Afra Shamnath, Mohamed Imran, Bani Jolly, Vinod Scaria
2021 bioRxiv   pre-print
This comprehensive repository encompasses a total of 532 variants accounting for 146 unique variants tested against 75 antibodies and patient convalescent plasma.  ...  We have a precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies.  ...  Compiled antibodies were systematically mapped back to the ABCD (for AntiBodies Chemically Defined) database which provides integrated information regarding the antibodies along with its corresponding  ... 
doi:10.1101/2021.02.18.431922 fatcat:sze3w25yrjbf5mx5h2bsztnow4

Mass spectrometry-based sequencing of the anti-FLAG-M2 antibody using multiple proteases and a dual fragmentation scheme [article]

Weiwei Peng, Matti F Pronker, Joost Snijder
2021 bioRxiv   pre-print
Here we demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products.  ...  Antibody sequence information is crucial to understanding the structural basis for antigen binding and enables the use of antibodies as therapeutics and research tools.  ...  obtain the recombinant antibody product with the four other monoclonal antibody sequences against the FLAG™ tag publicly available 207 through the ABCD (AntiBodies Chemically Defined) database 34-36 .  ... 
doi:10.1101/2021.01.07.425675 fatcat:52wpuljr3ffm3fnp44pzf4znxu

Prevalent mouse phenotypes in the unexplored druggable genome [article]

Olga Gulyaeva, Zicheng Hu, Tudor I Oprea, Kent Lloyd, Shawn M Gomez, Bryan L Roth, Michael McManus
2021 bioRxiv   pre-print
Among the estimated ~23,000 protein encoding human genes, the class of 'druggable genes', defined by their ability to bind drug-like compounds, represents an enticing collection of targets for clinical  ...  We show that both well-studied and understudied druggable genes share a similar number and spectrum of phenotypes.  ...  Acknowledgements We thank Lily Jan, John Gilchrist, all members of the McManus Lab who provided critical feedback during the course of this project.  ... 
doi:10.1101/2021.11.08.467777 fatcat:va7xaumjcbewrl6feaz2fll6re

Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

Astrid Wachter, Stephan Bernhardt, Tim Beissbarth, Ulrike Korf
2015 Microarrays  
Options for overcoming the downside of RPPA, which is the need to steadily validate new antibody batches, will be discussed.  ...  Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics.  ...  Acknowledgments The authors gratefully acknowledge financial support by BMBF e:Bio program grant MetastaSys (0316173) and by BMBF e:med grant HER2Low (031A429A).  ... 
doi:10.3390/microarrays4040520 pmid:27600238 pmcid:PMC4996411 fatcat:drtdmvbsfrbidegkbewttgx2i4

Current Approaches in Supersecondary Structures Investigation

Vladimir R. Rudnev, Liudmila I. Kulikova, Kirill S. Nikolsky, Kristina A. Malsagova, Arthur T. Kopylov, Anna L. Kaysheva
2021 International Journal of Molecular Sciences  
This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories  ...  for storage, as well as methods of molecular dynamics research.  ...  The information accumulated to date about proteins is summarized and arranged in public databases and repositories.  ... 
doi:10.3390/ijms222111879 pmid:34769310 pmcid:PMC8584461 fatcat:z6htmpbf3vfajc7b24lpguy7iy

Bacterial FtsZ induces mitochondrial fission in human cells [article]

Anna Spier, Martin Sachse, Nam To Tham, Mariette Matondo, Pascale Cossart, Fabrizia Stavru
2020 biorxiv/medrxiv   pre-print
Our results thus represent an innovative approach for the discovery of novel critical mitochondrial fission components.  ...  Here, we created a human codon optimized version of FtsZ, the central component of the bacterial division machinery, and fused it to a mitochondrial targeting sequence.  ...  Acknowledgements We would like to thank Véronique Hourdel and Quentin Giai Gianetto for initial analysis of mass spectrometry data and Ludmila Bonnand for help with live cell imaging analysis.  ... 
doi:10.1101/2020.01.24.917146 fatcat:qqqlrruk3zfg7ddwvtzcmtreyu

Biopanning [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
▶Copia b Barrel: The polypeptide chain of a membrane protein forms a folded up β sheet arranged in the shape of a barrel.  ...  /10) in the secretory pathway.  ...  Bispecific Monoclonal Antibodies (diabody): One of the two arms of the antibody has the recognition site for the surface antigens of a tumor cell, the other for the antigens of a killer lymphocyte.  ... 
doi:10.1007/978-1-4020-6754-9_1803 fatcat:5n2wlephrjf53m37xk6shlvlmq

Bryophytes [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
▶Copia b Barrel: The polypeptide chain of a membrane protein forms a folded up β sheet arranged in the shape of a barrel.  ...  /10) in the secretory pathway.  ...  Bispecific Monoclonal Antibodies (diabody): One of the two arms of the antibody has the recognition site for the surface antigens of a tumor cell, the other for the antigens of a killer lymphocyte.  ... 
doi:10.1007/978-1-4020-6754-9_2078 fatcat:lcaomb4wajf7xpyxilvwhjoeoi

Ideal Systems, Ideal Technology and their Realization Opportunities Using Information Communication & Computation Technology (ICCT) and Nanotechnology (NT)

P. Sreeramana Aithal
2021 Zenodo  
Technology management supports the use of technology for solving problems in society through innovations and to create a competitive advantage for the stakeholders.  ...  It is believed that the performance of a system and the capability of a technology can be continuously improved by means of comparing their properties with the properties of ideal system or ideal technology  ...  Green technologies are sustainable technologies which will not create a footprint when used for creating various products or processes. Green technologies support the use of natural  ... 
doi:10.5281/zenodo.4709634 fatcat:bvx7d7aax5aatnlayvnhuaozke

Study on the Concept of Ideal Systems, Ideal Technology and their Realization Opportunities using ICCT & Nanotechnology

Dr P. Sreeramana Aithal
2021 Zenodo  
Study on the Concept of Ideal Systems, Ideal Technology and their Realization Opportunities using ICCT & Nanotechnology: D.Sc. Thesis  ...  ABCD ANALYSIS IN EXPLORATORY RESEARCH : Exploratory research is research conducted for a problem that has not been clearly defined.  ...  as diseasefighting antibodies.  ... 
doi:10.5281/zenodo.5148343 fatcat:xupc6wlsabanjedtekzcqfpxla

Types of Disasters [chapter]

Paul N. Severin, Phillip A. Jacobson
2020 Nursing Management of Pediatric Disaster  
The Chemical Agents A chemical agent of terrorism is defined as any chemical substance intended for use in military operations to kill, seriously injure, or incapacitate humans (or animals) through its  ...  Basics of Explosions An explosion is defined as a rapid chemical conversion of a liquid or solid into a gas with energy release.  ... 
doi:10.1007/978-3-030-43428-1_5 fatcat:y3pszzuqtnddxeeozcv3d6wdei

D2.1_Mirri_Compilation Report On Outputs

R. Aznar, M. Fischer-Le Saux, E. Garay, D. Janssens, V. Piessens, C. Varese, A. Zuzuarregui
2014 Zenodo  
The feedback from MRCs/CCs will be used to determine which services and resources to include in the infrastructure and to lay down the requirements for resource/service providers.  ...  The design of MIRRI should be in accordance with the needs of the different user communities (academics, profit sector).  ...  [Accession numbers linking to genes or genomes in public sequence repositories (e.g. EMBL, GenBank); Links to protein databases (e.g. UniProt); Links to metabolic databases (e.g.  ... 
doi:10.5281/zenodo.49678 fatcat:cbvnd4mxfjaf7pokgwdxpernom

Scoring docking conformations using predicted protein interfaces

Reyhaneh Esmaielbeiki, Jean-Christophe Nebel
2014 BMC Bioinformatics  
In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure.  ...  Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use.  ...  The authors would also like to thank Qiangfeng Cliff Zhang and Lei Deng for providing PredUs data and Anna Panchenko, Raed Saeed Khashan, Thome Vreven, Brian Pierce and Rafael A Jordan for their helpful  ... 
doi:10.1186/1471-2105-15-171 pmid:24906633 pmcid:PMC4057934 fatcat:qudwqyjnjjcxboqktffr46tcl4
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