[AMBER] What would you like to see in visualization of chemical data?

From: Jan Mičan <honzamicann.gmail.com>
Date: Mon, 20 Jul 2020 12:48:06 +0200

Dearest AMBER user,

my name is Jan Mičan and I am (hopefully) a passionate computational
chemist like you. I am also working on molecular visualization software
development in VisITLab <http://visitlab.fi.muni.cz/>, where we are
developing better tools for intuitive visual analysis of molecular
dynamics, docking, and other chemical simulations data. It is bringing me
lots of joy to see my wishes of what I would need in visualization tools to
come true.

But why am I writing this email?

I am writing this email to know your wishes and dreams. In computational
chemistry, each one of us is focused on just some molecular properties,
protein families, etc...
Our ideas and perspectives are converging in the periodic boundary
conditions of our labs, topics of study, universities, towns, and
conferences we attend. If we could only know what all the voices which we
can't hear from there want! After some time of equilibration, we all start
to treat our solvent of perspectives implicitly.

We are in desperate need of a perturbation from YOU! We want you to know
what you would appreciate in visualizing your data.

Please tell me everything you would like to see in molecular visualization,
what would you like to be able to do, explore, and how would you like to
see your data, how these tools could help you.

For your appreciated help, I will send you a poem about the fantastic world
of molecular simulations dedicated to you.

Just for inspiration, I have written a paragraph that looks like
advertising our tools at first sight (which is against my principles of
course). However, it is here for inspiring you by ideas about what we do so
wishes about what would you like to see in molecular visualization appear
more easily.

Clever visualization and analysis tools can lead you to new ideas and
perspectives, make analysis way easier or it can make you able to make
analyses you could not before. Just to introduce you to what we do, we
develop a tool called CAVER Analyst
<https://pubmed.ncbi.nlm.nih.gov/29741570/> for viewing MD trajectories
with a special emphasis on tunnels and channels analysis and other handy
features such as caching which makes loading and analyzing very large
trajectories fast. We also have developed tools for interactive exploration
of protein unfolding <http://dx.doi.org/10.2312/vcbm.20161265>, visualizing
water trajectories
<https://diglib.eg.org/handle/10.2312/vcbm20171235>, Comparative
Visualization of Protein Secondary Structures
and much more <http://visitlab.fi.muni.cz/publications/>.

Thank you for reading this long email. I'll be thinking of you day and
night, waiting for your reply.

Yours faithfully,

Jan Mičan

Loschmidt Laboratories
Department of Experimental Biology & RECETOX
Faculty of Science, Masaryk University
Kamenice 5/A13, 625 00 Brno, Czech Republic
Faculty of Informatics, Masaryk University
Botanická 554/68a, 620 00 Brno, Czech Republic
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Received on Mon Jul 20 2020 - 04:00:03 PDT
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