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ABGEN specifications

Information


Unique identifier OMICS_15507
Name ABGEN
Alternative name AntiBody structure GENeration
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Windows
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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No version available

Publication for AntiBody structure GENeration

ABGEN citations

 (17)
library_books

How B Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

2017
Front Immunol
PMCID: 5727015
PMID: 29276518
DOI: 10.3389/fimmu.2017.01753

[…] the geometry of the binding site, allowing for the third step, which is modeling of non-H3 CDRs. At this stage, either the canonical classes are used () or template-based modeling such as FREAD () or ABGEN (). In the final step, CDR-H3 is modeled using either homology or ab initio techniques (). The resultant antibody model is refined for feasibility of dihedral angles from Ramachandran distributi […]

library_books

A transcriptional complex composed of ER(α), GATA3, FOXA1 and ELL3 regulates IL 20 expression in breast cancer cells

2017
Oncotarget
PMCID: 5522103
PMID: 28514748
DOI: 10.18632/oncotarget.17459

[…] cted with siRNA using siGENOME (Ell3, M-014601-01-0005; ER(α), L-003401-00-0010; GATA3, L-003781-00-0010; and FOXA1,L-010319-00-0010), which was provided by Dharmacon (distributed by ThermoScientific/AbGen, Epsom, UK). Cells were transfected with either target siRNA or non-specific siRNA using Lipofectamine 2000 (Invitrogen) in OPTI-MEM (Invitrogen) according to the manufacturer's instructions. […]

library_books

Antibody H3 Structure Prediction

2017
Comput Struct Biotechnol J
PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] el correctly, since it is thought to be mainly responsible for the antigen-binding properties of an antibody . While some algorithms exist that do not treat it any differently to the other CDRs (e.g. ABGEN ), this is not usual and a special approach is normally implemented, using a knowledge-based or ab initio approach, or some combination of the two. Some algorithms have tried to use the presence […]

library_books

Low glucose dependent decrease of apoptosis and induction of autophagy in breast cancer MCF 7 cells

2016
PMCID: 4887537
PMID: 27160935
DOI: 10.1007/s11010-016-2711-4

[…] Boston, USA), monoclonal (mouse) anti-human mTOR antibody (Merck-Millipore, USA), alkaline phosphatase-labeled anti-mouse immunoglobulin G by Rockland (PA, USA), polyclonal (rabbit) anti-human LC3 by Abgen, donkey anti-rabbit IgG conjugated with Alexa Fluor 488 by Molecular Probes (USA). […]

library_books

Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles

2016
PLoS One
PMCID: 4774998
PMID: 26934049
DOI: 10.1371/journal.pone.0150364

[…] Abcam ab19879), 1:100 Rabbit anti-USP13 (Abcam ab109264), 1:50 Rabbit anti-USP16 (Abcam ab135509), 1:100 Rabbit anti-USP22 (Abcam ab4812), 1:300 Rabbit anti-USP25 (in house), 1:250 Rabbit anti-USP28 (ABGEN AP2152b).1:500 for Mouse anti-Rhodopsin (Abcam, Cambridge, UK). Antibodies against AMSH (Biorbyt orb101007), JAB1 (Abcam ab12323), OTUB1 (Abcam ab76648), OTUD1 (Abcam ab122481), POH1 (Abcam ab80 […]

library_books

Recruited mast cells in the tumor microenvironment enhance bladder cancer metastasis via modulation of ERβ/CCL2/CCR2 EMT/MMP9 signals

2015
Oncotarget
PMCID: 4884958
PMID: 26556868
DOI: 10.18632/oncotarget.5467

[…] of 20 nM. Human CCL2 (MCP-1) recombinant protein was purchased from Affymetrix eBioscience (Santa Clara, CA, USA) and was adjusted to a final concentration of 10 nM. MMP9 inhibitor was purchased from ABGen and was adjusted to a final concentration of 5 μg/ml. […]

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ABGEN funding source(s)
This work was supported by research grant GM46535 from the National Institutes of Health.

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