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ABGEN specifications


Unique identifier OMICS_15507
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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Publication for AntiBody structure GENeration

ABGEN citations


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

PMCID: 5727015
PMID: 29276518
DOI: 10.3389/fimmu.2017.01753

[…] 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 […]


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

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

[…] 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., […]


Antibody H3 Structure Prediction

PMCID: 5312500
PMID: 28228926
DOI: 10.1016/j.csbj.2017.01.010

[…] 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 […]


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

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

[…] 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)., human breast cancer cell line mcf-7, which are estrogen receptor positive, were obtained from american type […]


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

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

[…] 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 […]


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

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

[…] 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., mast cell migration was examined using a 24-well transwell system. briefly, 1 × 106 bca cells or non-malignant sv-huc cells were plated […]

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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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