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Embracing Ambiguity:
Representation of Macromolecules Using the
Enhanced Standard HELM 2.0
Dr. Markus Weisser,
Co-Founder and Managing Director quattro research GmbH
The Pistoia Alliance
2
The Pistoia Alliance is a global, non-
profit alliance of life science
companies, vendors, publishers, and
academic groups that work together
to solve common problems and lower
barriers to innovation in R&D
3
quattro research
 Software and service company located in Munich,
Germany
 Tools and services for small and large molecules
 HELM know-how
 xHELM
 HAbE
 HELM 2.0
4
What is the HELM notation?
5
HELM is a line notation
that can encode the structure
of all biomolecules.
Why HELM notation?
6
G
A
P
N
NH
O
O
O
N
NH
O
O
O
Small
Molecules
Sequences
Biomolecules
Small Molecule Tools Sequence-Based Tools
Structure of the HELM notation?
7
Hierarchical Editing Language for Macromolecules
Complex Polymer Simple Polymer Monomer Atom
T. Zhang et al.
J.Chem. Inf. Model,
2012, 52(10), 2796
Syntax Elements
 $ separate HELM sections
polymers$connections$groupings$annotations
 . separate elements
PEPTIDE1{A.R.G.G.C.A}
 {}, [] and () are grouping characters
 ...
8
PEPTIDE1{A.R.G.[dF].C.K.[meA].E.D.A}$$$$
HELM Examples
9
PEPTIDE1{W.N.D.[T-est].G.[OR].D.A.D.G.S.[LM].[KYN]}|CHEM1{DA}$
PEPTIDE1,PEPTIDE1,13:R2-4:R3|PEPTIDE1,CHEM1,1:R1-1:R1$$$
Daptomycin
HELM history
10
HELM software ecosystem
11
HELMNotationToolkit
HELM
HELM Editor
HAbE
3rd Party Tools
ChemAxon
BioVia
PerkinElmer
Biochemfusion
ChEMBL
etc.
Mission completed?
12
???
 Unknown numbers of repeating elements
 Mixtures of sequences
 Unknown elements in sequences
 Unknown connections between polymers
 Undefined polymers
 ...
???
The HELM 2.0 project
 Initiated and founded by the Pistoia Alliance
 3 parts:
1. Support ambiguity for HELM
2. Remove dependency to closed source chemical toolkit
3. Switch to service oriented architecture by using REST
services
13
Ambiguity in HELM 2.0
1. Monomer ambiguity
Unknown monomers in a polymer
2. Polymer ambiguity
Sequence or polymer type is unknown
3. Connection ambiguity
The details of the connections between polymers are unknown
4. Grouping ambiguity
Unknown details of a grouping
14
Monomer Ambiguity
* 0..n unknown monomers PEPTIDE1{A.*.G.C}$$$$V2.0
X Single unknown amino acid in a
PEPTIDE
PEPTIDE1{A.X.G.C}$$$$V2.0
N Single unknown base in a RNA RNA1{R(A)P.R(N)P.R(C)P.R(C)P.R(C)}$$$
$V2.0
( , ) One of a list of monomer is possible PEPTIDE1{A.(A:10,G:90).G.C}$$$$V2.0
( + ) Mixture of monomers PEPTIDE1{A.(A+G+C).G.C}$$$$V2.0
_ Deleted or missing single monomer PEPTIDE1{A.(A,_).G.C}$$$$V2.0
´ ´ Repeating monomers PEPTIDE1{A.G.A.C.A‘5-30‘}$$$$V2.0
15
A G C
?
Polymer Ambiguity
 Sequence or polymer type is unknown
16
BLOB1{Bead}”Aminated Polystyrene”|PEPTIDE1{A.G.T}$$$$
A G T
Connection Ambiguity
 The details of the connections between polymers are
unknown
17
A small molecule binds to any Cysteine at peptide 1.
PEPTIDE1{A.A.A.A.A.A.C.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.
D.D.E.E.E.E.E.E.E.E.E.E.E.C.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G
.G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}|CHE
M1{[*]SCCCc1ccccc1 |$_R1;;;;;;;;;;$|}$PEPTIDE1,CHEM1,C:R3-1:R1$$
HELM NotationToolkit Re-Engineering
 New HELM parser
 Remove Marvin Beans dependency
 Service oriented architecture
18
HELM2NotationToolkit
Chemical Toolkit APIMarvinBeans
CDK 3rd party library
REST service API
HELMNotationToolkit
Marvin
Beans
HELM State Machine Parser
19
HELM Resources
20
https://github.com/PistoiaHELM
Example implementation
21
Example Implementation
22
Development Team
23
Development:
• Markus Weisser (quattro research)
• Sabrina Hecht (quattro research)
• Dmitry Chistyakov (quattro research)
Managment:
• Sergio Rotstein (Pfizer) – Domain Lead
• Claire Bellamy (Pistoia Alliance) – Project Manager
Pistoia Alliance HELM Team Members:
• Thomas Gan (Merck)
• Jan Holst Jensen (biochemfusion)
• Stefan Klostermann (Roche)
• Roland Knispel (ChemAxon)
• Jeff Milton (Ionis)
• Sven Neumeyer (Novartis)
• Matthias Nolte (BMS)
• Yohann Potier (Novartis)
• Eric Swayze (Ionis)
• Bernhard Schirm (quattro research)
• Tianhong Zhang (Pfizer)
Steering Committee Members:
• Margret Assfalg (Roche)
• Ramesh Durvasula (BMS)
• Leah O'Brien (GSK)
• Sergio Rotstein (Pfizer)
• Eric Swayze (Ionis)
• Chris Waller (Merck)
• John Wise (Pistoia Alliance)
• Quan Yang (Novartis)
References
 Poster presentation in the exhibit hall
 www.openhelm.org
 https://github.com/PistoiaHELM
 Zhang, Tianhong, et al.
Journal of chemical information and modelling 52.10 (2012): 2796-
2806
http://pubs.acs.org/doi/full/10.1021/ci3001925
24
Thank you!

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Enhanced Standard HELM 2.0

  • 1. Embracing Ambiguity: Representation of Macromolecules Using the Enhanced Standard HELM 2.0 Dr. Markus Weisser, Co-Founder and Managing Director quattro research GmbH
  • 2. The Pistoia Alliance 2 The Pistoia Alliance is a global, non- profit alliance of life science companies, vendors, publishers, and academic groups that work together to solve common problems and lower barriers to innovation in R&D
  • 3. 3
  • 4. quattro research  Software and service company located in Munich, Germany  Tools and services for small and large molecules  HELM know-how  xHELM  HAbE  HELM 2.0 4
  • 5. What is the HELM notation? 5 HELM is a line notation that can encode the structure of all biomolecules.
  • 7. Structure of the HELM notation? 7 Hierarchical Editing Language for Macromolecules Complex Polymer Simple Polymer Monomer Atom T. Zhang et al. J.Chem. Inf. Model, 2012, 52(10), 2796
  • 8. Syntax Elements  $ separate HELM sections polymers$connections$groupings$annotations  . separate elements PEPTIDE1{A.R.G.G.C.A}  {}, [] and () are grouping characters  ... 8 PEPTIDE1{A.R.G.[dF].C.K.[meA].E.D.A}$$$$
  • 11. HELM software ecosystem 11 HELMNotationToolkit HELM HELM Editor HAbE 3rd Party Tools ChemAxon BioVia PerkinElmer Biochemfusion ChEMBL etc.
  • 12. Mission completed? 12 ???  Unknown numbers of repeating elements  Mixtures of sequences  Unknown elements in sequences  Unknown connections between polymers  Undefined polymers  ... ???
  • 13. The HELM 2.0 project  Initiated and founded by the Pistoia Alliance  3 parts: 1. Support ambiguity for HELM 2. Remove dependency to closed source chemical toolkit 3. Switch to service oriented architecture by using REST services 13
  • 14. Ambiguity in HELM 2.0 1. Monomer ambiguity Unknown monomers in a polymer 2. Polymer ambiguity Sequence or polymer type is unknown 3. Connection ambiguity The details of the connections between polymers are unknown 4. Grouping ambiguity Unknown details of a grouping 14
  • 15. Monomer Ambiguity * 0..n unknown monomers PEPTIDE1{A.*.G.C}$$$$V2.0 X Single unknown amino acid in a PEPTIDE PEPTIDE1{A.X.G.C}$$$$V2.0 N Single unknown base in a RNA RNA1{R(A)P.R(N)P.R(C)P.R(C)P.R(C)}$$$ $V2.0 ( , ) One of a list of monomer is possible PEPTIDE1{A.(A:10,G:90).G.C}$$$$V2.0 ( + ) Mixture of monomers PEPTIDE1{A.(A+G+C).G.C}$$$$V2.0 _ Deleted or missing single monomer PEPTIDE1{A.(A,_).G.C}$$$$V2.0 ´ ´ Repeating monomers PEPTIDE1{A.G.A.C.A‘5-30‘}$$$$V2.0 15 A G C ?
  • 16. Polymer Ambiguity  Sequence or polymer type is unknown 16 BLOB1{Bead}”Aminated Polystyrene”|PEPTIDE1{A.G.T}$$$$ A G T
  • 17. Connection Ambiguity  The details of the connections between polymers are unknown 17 A small molecule binds to any Cysteine at peptide 1. PEPTIDE1{A.A.A.A.A.A.C.A.A.A.A.A.A.A.A.A.A.A.A.A.A.C.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D.D. D.D.E.E.E.E.E.E.E.E.E.E.E.C.E.E.E.E.E.E.E.E.E.E.E}|PEPTIDE2{G.G.G.G.G.G.G.G.G.G.G.G.G.G.G .G.G.G.G.G.G.G.G.G.G.C.S.S.S.S.S.S.S.S.S.P.P.P.P.P.P.P.P.P.K.K.K.K.K.K.K.K.K.K.K.K.K}|CHE M1{[*]SCCCc1ccccc1 |$_R1;;;;;;;;;;$|}$PEPTIDE1,CHEM1,C:R3-1:R1$$
  • 18. HELM NotationToolkit Re-Engineering  New HELM parser  Remove Marvin Beans dependency  Service oriented architecture 18 HELM2NotationToolkit Chemical Toolkit APIMarvinBeans CDK 3rd party library REST service API HELMNotationToolkit Marvin Beans
  • 19. HELM State Machine Parser 19
  • 23. Development Team 23 Development: • Markus Weisser (quattro research) • Sabrina Hecht (quattro research) • Dmitry Chistyakov (quattro research) Managment: • Sergio Rotstein (Pfizer) – Domain Lead • Claire Bellamy (Pistoia Alliance) – Project Manager Pistoia Alliance HELM Team Members: • Thomas Gan (Merck) • Jan Holst Jensen (biochemfusion) • Stefan Klostermann (Roche) • Roland Knispel (ChemAxon) • Jeff Milton (Ionis) • Sven Neumeyer (Novartis) • Matthias Nolte (BMS) • Yohann Potier (Novartis) • Eric Swayze (Ionis) • Bernhard Schirm (quattro research) • Tianhong Zhang (Pfizer) Steering Committee Members: • Margret Assfalg (Roche) • Ramesh Durvasula (BMS) • Leah O'Brien (GSK) • Sergio Rotstein (Pfizer) • Eric Swayze (Ionis) • Chris Waller (Merck) • John Wise (Pistoia Alliance) • Quan Yang (Novartis)
  • 24. References  Poster presentation in the exhibit hall  www.openhelm.org  https://github.com/PistoiaHELM  Zhang, Tianhong, et al. Journal of chemical information and modelling 52.10 (2012): 2796- 2806 http://pubs.acs.org/doi/full/10.1021/ci3001925 24 Thank you!