The HELM Antibody Editor allows the user to visualise and manipulate antibody structures.
It includes many features, but the ability to detect domains and add structural features such as Cys-Cys bonds is central.
**New** HAbE2
HAbE2 was released to GitHub in January 2018. Many thanks again to Roche who have continued to develop the antibody editor and have donated their efforts to the open source community.
Key new features include:
MonomerDesigner:
Design your own new monomer for the HAbE and save it into your local monomer store
ADCDesigner
Attach chemical molecules to a peptide at the N- or C-terminal end, on specific amino acids or on an amino acid type with a statistical binding ratio
Domain Protease Reaction
Cut your antibody according to the protease sequence motif
Sortase Coupling
Split your antibody according to a peptide motif and connect it with a ligand
Biotinylation
Covalently attach biotin to AVI-tag
Domain Protease Reaction
Cut your antibody according to the protease sequence motif
Sortase Coupling
Split your antibody according to a peptide motif and connect it with a ligand
Biotinylation
Covalently attach biotin to AVI-tag
Getting started
The following documents provide an overview of the antibody editor and the functionality available.
HELM Antibody Editor: What is it, what can it do? (slides)
Extended Overview of HAbE (slides)
User guides
User guide for the HELM Antibody Editor (document)
Source Code
All code is published in GitHub
HAbE2 : https://github.com/PistoiaHELM/HELMAntibodyEditor2
Example Plugins : https://github.com/PistoiaHELM/HELMAntibodyEditor2Plugin
Compiled code - try it for yourself
- Compiled code can be found in the release folder in GitHub
Technical information
How to connect to the domain / mutation / rule libraries when located in a database
Custom Master Libraries in HAbE v2.pdf
How to write plugins e.g. to store the antibody constructs in databases instead of XML files
How to write plugins for HAbE v2.pdf
Licenses and restrictions
HELM is an open source project released under the MIT license. However it currently has some dependencies on third party tools.
- HELM Editor requires yFiles for Java version 2.6 or higher and GraphML extension from yWorks. If you wish to use the compiled software directly there is no need to buy a licence. If you wish to develop the software for your own use, trial versions of such libraries can be downloaded from yWorks at www.yworks.com. You need to update the ant build file with regard to yfiles.dir and jar file names before compiling and running the project.
The HELM Toolkit requires MarvinBeans version 5.0 or higher from ChemAxon. A copy of the required library (MarvinBeans-5.0.jar) is included for your convenience. ChemAxon has graciously agreed to provide a royalty-free license for the utilization of MarvinBeans directly through the HELM editor and notation toolkit (specifically for operations pertaining to the chemical representation of HELM monomers and macromolecules.) Please contact Cassell Essell (cessell@chemaxon.com) to obtain this license. Utilization of the MarvinBeans library outside of the aforementioned scope and beyond a trial basis requires the procurement of a regular MarvinBeans license.
The project is actively working to remove these restrictions. We welcome anyone who wishes to contribute to the project by replacing any of these components.