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Exchangeable HELM
Markus Weisser
at HELM Showcase Webinar
Status quo HELM notation
flexible for different types of biomolecules
compact notation
human readable
not self-contained
2
HELM use case pharma company
3
Monomer database
HELM use case in small organizations
4
Local
Monomer
Store
Local
Monomer
Store
Collaboration between pharma and CRO
5
Monomer database
Local
Monomer
Store
Request for proposal for Exchangeable HELM
from Pistoia Alliance
1. Definition of exchangeable HELM notation (xHELM)
2. Mo...
Status quo HELM toolkit/editor
 Create, edit, load and save HELM notation
 Register monomers in local ‘database’ (xml do...
Exchangeable HELM – XML container for HELM
notation and monomer information
8
Local
Monomer
Store
xHELM
HELM notation
Mono...
xHELM structure
9
Xhelm
HelmNotation
Monomers
Monomer
MonomerID
MonomerSmiles
MonomerMolFile
MonomerType
PolymerType
Natur...
xHELM example
10
<?xml version="1.0" encoding="UTF-8"?>
<Xhelm>
<HelmNotation>PEPTIDE1{A.G}$$$$</HelmNotation>
<Monomers>
...
xHELM support in HELM toolkit and editor
 Load and save HELM as well as xHELM
11
xHELM
HELM
New monomers from xHELM
12
Monomer Modification and inline SMILES notation
13
HELM inline SMILES notation
 Existing SMILES inline notation for chemical monomers
extended for all monomer types.
 Exte...
Monomer Registration from xHELM and inline
SMILES
 Checking for mismatches and uniqueness
15
Local
Monomer
Store
xHELM
In...
Collaboration between pharma and CRO
16
Monomer database
Local
Monomer
Store
xHELM
Project Summary
 Definition and implementation of exchangeable HELM
format
 HELM toolkit and editor support for xHELM
 ...
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Exchangeable HELM as a new standard for biomolecules

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Exchangeable HELM

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Exchangeable HELM as a new standard for biomolecules

  1. 1. Exchangeable HELM Markus Weisser at HELM Showcase Webinar
  2. 2. Status quo HELM notation flexible for different types of biomolecules compact notation human readable not self-contained 2
  3. 3. HELM use case pharma company 3 Monomer database
  4. 4. HELM use case in small organizations 4 Local Monomer Store Local Monomer Store
  5. 5. Collaboration between pharma and CRO 5 Monomer database Local Monomer Store
  6. 6. Request for proposal for Exchangeable HELM from Pistoia Alliance 1. Definition of exchangeable HELM notation (xHELM) 2. Modification HELM editor for exchangeable HELM 3. Support inline SMILES notation for all types of monomers 4. Registration of new monomers from exchangeable HELM 6
  7. 7. Status quo HELM toolkit/editor  Create, edit, load and save HELM notation  Register monomers in local ‘database’ (xml document)  Modify chemical monomers (inline SMILES) 7 Local Monomer Store
  8. 8. Exchangeable HELM – XML container for HELM notation and monomer information 8 Local Monomer Store xHELM HELM notation Monomers HELM Specification 1_1.doc http://www.openhelm.org/HELM_Notation
  9. 9. xHELM structure 9 Xhelm HelmNotation Monomers Monomer MonomerID MonomerSmiles MonomerMolFile MonomerType PolymerType NaturalAnalog MonomerName Attachments Attachment AttachmentID AttachmentLabel CapGroupName CapGroupSmiles
  10. 10. xHELM example 10 <?xml version="1.0" encoding="UTF-8"?> <Xhelm> <HelmNotation>PEPTIDE1{A.G}$$$$</HelmNotation> <Monomers> <Monomer> <MonomerID>A</MonomerID> <MonomerSmiles>C[C@H](N[*])C([*])=O |$;;;_R1;;_R2;$|</MonomerSmiles> <MonomerMolFile>H4sIAAAAAA…</MonomerMolFile> <MonomerType>Backbone</MonomerType><PolymerType>PEPTIDE</PolymerType> <NaturalAnalog>A</NaturalAnalog><MonomerName>Alanine</MonomerName> <Attachments> <Attachment> <AttachmentID>R2-OH</AttachmentID><AttachmentLabel>R2</AttachmentLabel> <CapGroupName>OH</CapGroupName><CapGroupSmiles>O[*] |$;_R2$|</CapGroupSmiles> </Attachment> <Attachment> <AttachmentID>R1-H</AttachmentID><AttachmentLabel>R1</AttachmentLabel> <CapGroupName>H</CapGroupName><CapGroupSmiles>[*][H] |$_R1;$|</CapGroupSmiles> </Attachment> </Attachments> </Monomer> <Monomer> <MonomerID>G</MonomerID> <MonomerSmiles>[*]NCC([*])=O |$_R1;;;;_R2;$|</MonomerSmiles> <MonomerMolFile>H4sIAAAAAAAAAKWSP…</MonomerMolFile> <MonomerType>Backbone</MonomerType><PolymerType>PEPTIDE</PolymerType> <NaturalAnalog>G</NaturalAnalog><MonomerName>Glycine</MonomerName> <Attachments> <Attachment> <AttachmentID>R2-OH</AttachmentID><AttachmentLabel>R2</AttachmentLabel> <CapGroupName>OH</CapGroupName><CapGroupSmiles>O[*] |$;_R2$|</CapGroupSmiles> </Attachment> <Attachment> <AttachmentID>R1-H</AttachmentID><AttachmentLabel>R1</AttachmentLabel> <CapGroupName>H</CapGroupName><CapGroupSmiles>[*][H] |$_R1;$|</CapGroupSmiles> </Attachment> </Attachments> </Monomer> </Monomers> </Xhelm>
  11. 11. xHELM support in HELM toolkit and editor  Load and save HELM as well as xHELM 11 xHELM HELM
  12. 12. New monomers from xHELM 12
  13. 13. Monomer Modification and inline SMILES notation 13
  14. 14. HELM inline SMILES notation  Existing SMILES inline notation for chemical monomers extended for all monomer types.  Extended SMILES notation in square brackets  Example: PEPTIDE1{G.A.T}$$$$ → PEPTIDE1{G.[C[13C@H](N[*])C([*])=O |$;;;_R1;;_R2;$|].T}$$$$ 14
  15. 15. Monomer Registration from xHELM and inline SMILES  Checking for mismatches and uniqueness 15 Local Monomer Store xHELM Inline SMILES
  16. 16. Collaboration between pharma and CRO 16 Monomer database Local Monomer Store xHELM
  17. 17. Project Summary  Definition and implementation of exchangeable HELM format  HELM toolkit and editor support for xHELM  Definition and implementation of inline SMILES for all monomer types  Inline editing of all types of monomers in editor  Registration of new monomers out of xHELM and inline SMILES notation 17

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