LiteMol suite – real-time web-based
visualization of large macromolecular
structural data
pdbe.org & ncbr.muni.cz/LiteMol2
pdbe.org & ncbr.muni.cz/LiteMol3
Bring the viewing experience
to the web browser
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PDB
125k entries, +10% per year
Big entries:
• HIV-1 capsid (3j3q), 2.4M atoms
• Aquareovirus virion (3k1q)
assembly, 6M atoms
More large systems will be
resolved: ribosomes, viruses, etc.
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HIV-1 capsid
Aquareovirus virion
pdbe.org & ncbr.muni.cz/LiteMol5
pdbe.org & ncbr.muni.cz/LiteMol
ENTIRE STRUCTURE or an INTERESTING PART
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pdbe.org & ncbr.muni.cz/LiteMol
MODEL, EXPERIMENTAL DATA, and ANNOTATION
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pdbe.org & ncbr.muni.cz/LiteMol
Data delivery
takes a long time
Visualization
is computationally demanding
User interaction
must be pleasant
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The solution is obvious…
Send only the relevant data
Compress
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LiteMol suite
3D coordinate data
Experimental data (density)
Annotation API
Data compression
Visualization
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Viewer
VISUALIZATION
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pdbe.org & ncbr.muni.cz/LiteMol12
Viewer
pdbe.org & ncbr.muni.cz/LiteMol
LiteMol
Web browser based 3D visualization plugin
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Common 3D
atomic models,
assemblies,
symmetry
Density maps
and Cryo-EM
data
Validation
data,
sequence
annotation
…and it’s fast
pdbe.org & ncbr.muni.cz/LiteMol
LiteMol in PDBe
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pdbe.org/1qrw (3D visualization)
DATA DELIVERY
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pdbe.org & ncbr.muni.cz/LiteMol
Coordinate Server
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On-demand 3D molecular structure
• backbone, individual entities or chains
• ligand interactions
• assemblies, symmetry mates
pdbe.org & ncbr.muni.cz/LiteMol
Coordinate Server
https://www.ebi.ac.uk/pdbe/coordinates
/1gzt/ligandInteraction?name=FUC
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pdbe.org & ncbr.muni.cz/LiteMol
BinaryCIF
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• An efficient way of storing
macromolecules and other data
• Compatible with the mmCIF standard
42MB CIF 1.5-12MB
pdbe.org & ncbr.muni.cz/LiteMol
Example: Delivery of HIV-1 capsid
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HIV-1 capsid, 2.44M atoms
(PDB ID 3j3q)
Download + Visualization time:
• Full (42 MB):
• 60s
pdbe.org & ncbr.muni.cz/LiteMol
Example: Delivery of HIV-1 capsid
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HIV-1 capsid, 2.44M atoms
(PDB ID 3j3q)
Download + Visualization time:
• Full (42 MB):
• 60s
• Coordinate Server + BinaryCIF
(0.6M atoms, 1.5 MB):
• 10s
• 27x less data
pdbe.org & ncbr.muni.cz/LiteMol21
pdbe.org & ncbr.muni.cz/LiteMol
PDBe Ligand Pages
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www.ebi.ac.uk/pdbe/entry/pdb/3bur/bound/TES
EXPERIMENTAL DATA
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pdbe.org & ncbr.muni.cz/LiteMol
DensityServer
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• On-demand experimental data
• Instantly access any slice of available density
• Uses the BinaryCIF format
• Works in a way similar to the CoordinateServer
pdbe.org & ncbr.muni.cz/LiteMol
DensityServer Example
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Fully Refined Crystal Structure of the Haloarcula marismortui
Large Ribosomal Subunit at 2.4 Å Resolution (X-ray, PDB id
1JJ2)
• 145MB of CCP4 density data, 10+s latency
• 5Å around any residue: 10-30KB, 150ms latency
pdbe.org & ncbr.muni.cz/LiteMol
DensityServer Example
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Life in the extremes: atomic structure of Sulfolobus Turreted
Icosahedral Virus (2.7M atoms, Cryo-EM, PDB id 3j31)
• 4GB of CCP4 density data
• 50Å sphere anywhere: 400KB in <0.5s
pdbe.org & ncbr.muni.cz/LiteMol
Uppsala Electron Density Server retired
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pdbe.org/eds
AstexViewer (Java)
ANNOTATION
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pdbe.org & ncbr.muni.cz/LiteMol
Validation and Sequence Annotation
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Nipah Virus G Attachment Glycoprotein
3D12
PDBe validation score UNIPROT annotation
Chloride Channel Complex
5T5N
pdbe.org & ncbr.muni.cz/LiteMol
Interactive 1D, 2D and 3D structure
www.ebi.ac.uk/pdbe/entry/pdb/1cbs/protein/1
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IT’S FOR EVERYONE
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pdbe.org & ncbr.muni.cz/LiteMol
It’s for everyone
• Accessible from PDBe and LiteMol Viewer
• Services can be consumed by 3rd parties
• LiteMol in your applications
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pdbe.org & ncbr.muni.cz/LiteMol
Summary
• Rich visualization available in the web
browser
• Integrated into PDBe
• Available for everyone
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