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ABangle specifications

Information


Unique identifier OMICS_04188
Name ABangle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Charlotte Deane

Information


Unique identifier OMICS_04188
Name ABangle
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Charlotte Deane

Publication for ABangle

ABangle citations

 (9)
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 second step is determining the VH/VL orientation, which can be achieved by copying the orientation angle from structures with high Fv sequence identity using VH/VL orientation methods such as AbAngle (), analytical estimation of the angle using energy functions (), tailored protein–protein docking () or structure-trained machine learning (). Once the VH/VL orientation is set, it constrains […]

library_books

Fully automated antibody structure prediction using BIOVIA tools: Validation study

2017
PLoS One
PMCID: 5436848
PMID: 28542300
DOI: 10.1371/journal.pone.0177923

[…] ion causes the inaccurate orientation of the domains.4CNI_BA and 4FZE_LH may be outliers for tilt angle because they adopt VL-VH orientations towards the extremes of the distributions found using the ABangle webserver [] for at least one of its measures. In the case of 4FZE, this is particularly marked for the HL angle, whereas for the template 4JZO (which is used twice as it exists in two slightl […]

library_books

DynaDom: structure based prediction of T cell receptor inter domain and T cell receptor peptide MHC (class I) association angles

2017
BMC Struct Biol
PMCID: 5289058
PMID: 28148269
DOI: 10.1186/s12900-016-0071-7

[…] free and the MHC bound forms of TCRs constitute a feature of the receptor to adapt to different ligands, thus allowing cross reactivity []. Dunbar et al. analyzed a non-redundant set of TCRs with the ABangle methodology [], which describes both the Vα- and the Vβ-orientation in an absolute manner, by considering a torsion angle, four bend angles and one distance as descriptors []. In the context o […]

library_books

Computational design of an epitope specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

2017
Sci Rep
PMCID: 5269676
PMID: 28128368
DOI: 10.1038/srep41306

[…] acking between CDRH3, L2 loops and blade 4 of Keap1 from the neighbouring crystal unit (). This unexpected VH/VL orientation change was also characterised using the structural descriptors computed by ABangle, and the most notable difference is observed in the VH/VL torsional angle with a 10° deviation between the crystal and modelled structures, and detectable difference in terms of bend angles of […]

library_books

Applicability of predictive toxicology methods for monoclonal antibody therapeutics: status Quo and scope

2016
PMCID: 5364268
PMID: 27766364
DOI: 10.1007/s00204-016-1876-7

[…] nteraction fingerprint (EPIF) which tries to address the higher time-complexity of MLPD, thus allowing for simplification the antigen–antibody interaction term (Qiu et al. , ). Platforms like proABC, ABangle and LYRA allow for modelling antigen–antibody interactions, orientation of variable chain and lymphocyte receptor, respectively (Klausen et al. ; Olimpieri et al. ; Dunbar et al. ). Physicoche […]

library_books

Structural diversity in a human antibody germline library

2016
MAbs
PMCID: 4968113
PMID: 27210805
DOI: 10.1080/19420862.2016.1190060

[…] h calculates the 6 VH:VL orientation parameters that describe the VH:VL relationship according to Dunbar and co-workers using a script downloaded from the website (http://opig.stats.ox.ac.uk/webapps/abangle). The six parameters include 5 angles, HL, H1, H2, L1 and L2, and a distance, dc. These parameters are derived by first defining 2 planes, one for each domain, based on core residues in the do […]

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ABangle institution(s)
Department of Statistics, University of Oxford, Oxford, UK
ABangle funding source(s)
This work was supported by the Engineering and Physical Sciences Research Council, Roche Diagnostics GmbH and UCB Pharma.

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