Visualisation techniques are used in the area of small molecules, drug molecules, protein and to understand complex functions and interaction points to infer the mechanisms

1. Visualization Tools : An Overview
Girinath G. Pillai, PhD
Coordinator DDH2020, MHRD Govt of India.
@giribio

2. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Note
Slides contains contents/pictures/videos taken from web, articles, lectures, tutorials
and its respective authors own their copyrights.
Technical Slides : slideshare.net/giribio
Handson Videos : youtube.com/giribio (Autodock, Modeller, PaDel, QSAR, MD, etc)
Workflows & Notebooks : github.com/giribio
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3. What to expect?
● What is Visualization
● Role of Viz in Drug Discovery
● Image Processing
● Viz Chemical Structures
● Viz Cheminformatics Data
● Viz Chemical Space
● Viz Proteins/Interactions/MD
● Case Studies
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4. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Why Visualization is Important?
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● What ideas these visualizations trying to communicate?
● Learning objectives
● Graphical or schematics
● 2D or 3D representations
● When experimental data is not available, we choose data-driven-structures
● Structure determines functions

5. Tools to support
Visualization
Protein, Small Molecules,
etc
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6. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Data/Image Processing
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7. Chemical
Structures
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8. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
OSRA
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● OSRA: Optical Structure Recognition Application
● Convert graphical representations of chemical
structures
● From journal articles, patent documents, textbooks,
trade magazines etc.
● Read documents like GIF, JPEG, PNG, TIFF, PDF, PS etc.
● Generates SMILES or SD files
● Curation by a human knowledgeable in chemical
structures is highly recommended.
● Free and Open Source Downloadable Linux Software
● Web Interface
https://cactus.nci.nih.gov/osra/
J Chem Inf Model. 2009 Mar; 49(3): 740–743.

9. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Marvin Sketch
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● A featured chemical editor for making science
accessible on all platforms
● Drawing chemical compounds
● Import Export multiple file formats
● Structure display and Journal formats
● MarvinView
● Molconvert
● Freemium - check with providers!
https://chemaxon.com/products/marvin

10. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
ChemSketch
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● Comprehensive Chemical Drawing Package
● Drawing chemical compounds
● Identify Tautomers
● 3D View etc
● Freemium - Free Edu/Academic license
https://www.acdlabs.com/resources/freeware/chemsketch/

11. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
BIOVIA Draw
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● To draw and edit complex molecules
● Capabilities for managing complex biological
entities including the ability to register and retrieve
peptides, oligonucleotides, and oligosaccharides
● Add-ins include tools for molecular property
calculation/prediction, enumeration, bioavailability,
isotopomer distribution, and stoichiometry
calculations, and many more.
● Freemium - Free Edu/Academic license
https://discover.3ds.com/biovia-draw-academic

12. Cheminformatics
Data
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13. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
DataWarrior
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● Open-Source Program for Data Visualization and
Analysis with Chemical Intelligence
● Interactive data visualization and analysis
● Built-in chemical intelligence
● Real Time data filtering on alphanumerical and
chemical criteria
● Prediction of molecular properties from the
chemical structure
● Dedicated cheminformatics modules support drug
discovery
● Free to use without commercialization
http://www.openmolecules.org/datawarrior/

14. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
KNIME
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● Analytics platform - an open source software for
creating data science
● Access, merge and transform all of your data
● Make sense of your data with the tools you
choose - Model and Visualise
● Leverage insights gained from your data -
Optimise
● Several extensions / nodes for cheminformatics,
bioinformatics, QSAR, machine learning,
statistical modelling, etc
● Free - Nodes/Extensions could be proprietary
https://www.knime.com/downloads/download-knime

15. 3D Visualizers
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Proprietary but free
academic/education license

16. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Chimera
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● Interactive visualization and analysis of
molecular structures and related data.
● High-quality images and animations
● Chimera Interface to Modeller
● CASTp Pocket Data
● Structure-Based Sequence Alignment
● Superimposing structures
● UCSF ChimeraX (or simply ChimeraX) is the
next-generation molecular visualization
program with VR and ambient occlusions
● Free for all
https://www.cgl.ucsf.edu/chimera/download.ht
ml

17. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
VMD
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● A molecular visualization program for displaying,
animating, and analyzing large biomolecular
systems
● Interface to NAMD
● MD data analysis
● Collective Variables Interface
● Freemium - Free Edu/Academic license
https://www.ks.uiuc.edu/Research/vmd/

18. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
MGL Tools - PMV
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A molecular visualization program for displaying,
animating, and analyzing biomolecular systems
Interface to AutoDock, AutoDock Vina
Preparation of data
Freemium - Free Edu/Academic license
http://mgltools.scripps.edu/downloads

19. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
PyMol
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● A stand-alone molecular visualization program
that is very popular with protein
crystallographers because of the high quality of
its rendering, its speed and versatility
● Labeling, editing and representations
● Open Source & Free to Education only
https://pymol.org/edu/

20. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Avogadro
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● An advanced molecule editor and visualizer
designed for cross-platform use in
computational chemistry, molecular modeling,
bioinformatics, materials science, and related
areas.
● Flexible high quality rendering and a powerful
plugin architecture.
● Conformer generation, optimization, etc
● Free, Open Source
https://pymol.org/edu/

21. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
NGLView
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● NGL Viewer is a collection of tools for web-
based molecular graphics.
● WebGL is employed to display molecules like
proteins and DNA/RNA with a variety of
representations.
● Jupyter/IPython widget
● MDsrv is a web-based tool
● MDtraj
● Pytraj
http://nglviewer.org/

22. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
Additional Visualizers
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● Jmol, Rasmol, SwissPDB Viewer, etc
● Maestro - Free Visualizer for academics
● Discovery Studio Visualizer - Free for academics
● ICM Browser - Free for academics
● Flare Viewer - Free for academics

23. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
PoseView
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https://proteins.plus/

24. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
LigPlot+
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https://www.ebi.ac.uk/thornton-srv/software/LigPlus/

25. Principles of
Visualization
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Selected 10 Principles

26. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
1: Molecules move through random collisions
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Molecules move around through collisions resulting in random
Brownian motion. In this eg, A, an Arp2/3 complex moves
smoothly and linearly before binding to an actin filament, whereas
in B, the motion is complex and chaotic.
Consider depicting random walks.
A B

27. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
2: Molecules are in constant motion
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Newton’s first law states that objects remain in motion without external forces.
While molecules are subjected to constant forces from all sides, the result is
they are in constant motion and do not start and stop spontaneously. In this eg,
in A, CRAF, MEK, and ERK, components in a signalling cascade are not moving
unless they are involved in binding, whereas in B, they continue moving, even
when not immediately involved in the process.
Consider keeping molecules moving.
A B

28. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
3: Intermolecular attractions are local forces
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Relative motion between two binding partners. In this eg, in A, Na ions flow
towards and traverse a voltage-gated ion channel as though attracted by a
magnetic force, whereas in B, they move through the channel through local
collisions and interactions with the transmembrane channel.
Consider ensuring that distant molecules are unaffected by pulling forces.
A B

29. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
4: Unproductive collisions occurs more
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Not every encounter between complementary molecules results in binding;
in fact statistically there are likely to be many more unproductive collisions
than productive ones. In this eg, in A, Sos and Ras come together and bind
on first encounter, whereas in B, they collide a number of times before
their orientations result in tight binding.
Consider including non-binding collisions.
A B

30. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
5: Many instances of molecules and events exist
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Typically many instances of molecules and events present in a given
environment; repetition can also reinforce the process being depicted.
In this eg, in A, only one copy each of siderocalin and enterobactin are
shown, which bind together, whereas in B, there are several copies of
each, and multiple binding events.
Consider presenting multiple copies.
A B

31. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
6: Not all instances of a molecule change states
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Not every molecule is used in a process or
changes its state. More monomers are
present than will be incorporated into a
polymer, and typically more substrates are
present than will be converted into a product.
Likewise, not all molecules will cross a barrier
or will bind to a chelator. In this eg, in A, all
subunits form a single viral capsid, whereas in
B, once the capsid is complete, there are still
subunits that remain.
Consider leaving some molecules behind.

32. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
7: Molecular landscapes are crowded and diverse
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Cellular environments are busy and crowded, with very little empty space,
particularly if molecular water is included. Even without the depiction of
molecular water, macromolecules take up a sizeable % of the volume. In this
eg, in A, a PTPS molecule moves in an intracellular environment consisting
of actin filaments and a nucleus, whereas in B, a diverse suite of proteins,
RNA, metabolites and more fill the surrounding cytoplasmic space.
Consider populating molecular environments with macromolecules.

33. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
8: Molecules are physical entities with defined boundaries
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Molecules are physical entities with definable boundaries. Intersecting surface
meshes provide conflicting or obscured information about interaction and binding
sites. In this eg, in A, a PCNA DNA clamp slides along a DNA strand with coarse
meshing that overlaps with itself and with the DNA, whereas in B, the meshes are
tightly defined and show space between the clamp and DNA, indicating intermolecular
forces that keep the molecules from occupying the same space.
Consider respecting atomic boundaries with surface meshes.
A B

34. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
9: Proteins exhibit a range of flexibility
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Proteins have internal freedom of motion that allows for specific
functionality. Some parts of a protein are more flexible than others and
some proteins are more rigid than others. In this eg, in A, the membrane
protein cadherin moves in the membrane, but is internally rigid, whereas in
B, the five extracellular domains are linked by short flexible regions.
Consider showing protein flexibility.
A B

35. June 18, 2021 Girinath G. Pillai, PhD | Workshop on Visualization
@giribio
10: Many binding reactions are reversible
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Molecules do not bind permanently and many reactions are reversible at
the individual molecule level. In this eg, in A, the mTORC1 complex
phosphorylates its substrate S6K1 the first time that it binds in every
case, whereas in B, the substrate dissociates and binds again before
being phosphorylated.
Consider including some unproductive binding and dissociation.
A B

36. Thank you!
Dr. Abhay Jere
Prof. Narahari Sastry, Dr. Nagamani, Lijo & Team
Dr. Kunal Roy
Dr. Amit Prasad
Dr. Srinivas
Mr. Rajeev Gangal
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Do you have any questions?
gpillai@zastrain.com
+91 94483 67493
www.zastrain.com
@giribio
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