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 is now available in GitHub. 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

All about HAbE

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.

Case Study