Dear Amber Users!
On behalf of Tunneling Group, I would like to invite you all to the first
edition of the
*AQUA-DUCT WEBINAR OF MOLECULAR DYNAMICS SIMULATIONS ANALYSIS WITH
MOLECULAR PROBES*
http://www.aquaduct.pl/webinar/
<
http://www.aquaduct.pl/webinar/?fbclid=IwAR0Zi2Yx5BaE7fE6pP5D-xAyh42rnqb1YA67d3Dlb-FepX3rBOQRbD3izMY>
The webinar will take place on *the Zoom *platform *on 23rd September 2020*.
For participants from Asia and Australia the webinar will be held at *10 am*
(*GMT+2*, Warsaw time) and for participants from Europe, Africa, North, and
South America, the webinar will be held at *5 pm* (*GMT+2*, Warsaw time).
The expected duration of the webinar is approximately 2 hours.
The participation is free of charge, you just need to register here:
https://docs.google.com/forms/d/1or8ZDpUnrNM9wU924glzlYJPhmQs1MeFOaCg8_qFfyU
<
https://docs.google.com/forms/d/1or8ZDpUnrNM9wU924glzlYJPhmQs1MeFOaCg8_qFfyU?fbclid=IwAR0Zi2Yx5BaE7fE6pP5D-xAyh42rnqb1YA67d3Dlb-FepX3rBOQRbD3izMY>
The link to the event will be sent to registered participants one week
before the webinar (16th September 2020), and the remainder will be sent
one day before the webinar.
Topics covered:
i) AQUA-DUCT – general information, functionality, workflow
ii) Introduction to AQUA-DUCT calculations
iii) Molecular probes applicability in protein engineering and in drug
design (e.g., solvent transport analysis, inner void analysis, hot-spots
analysis)
iv) Q&A session
Information about the webinar:
Molecular dynamics simulations are widely used as a versatile research
method. Many additional tools were developed to facilitate and extend the
analysis of MD simulations. AQUA-DUCT is one of the unique tools, that
reverses the standard approach of describing the evolution of
macromolecules’ dynamics. Instead of their atoms’ movement analysis, it
enables an investigation from the perspective of “intramolecular voids”. To
achieve this goal, AQUA-DUCT samples macromolecules’ dynamics employing
molecular probes – small entities in simulations (most frequently water
molecules, but it could be any solvent, co-solvent, ions, or other
ligands). The small molecules are used as specific chemical probes. The
mixed “ligands-tracking” and “local-distribution” approaches implemented in
AQUA-DUCT allow discrimination between functionally relevant compartments,
and provide direct access to information about the active site, potential
hot-spots, functional residues (gates, anchoring residues, filters, etc.),
the network of internal transportation pathways, and functional voids and
cavities. Besides that, it can facilitate the drug design process. The
webinar will provide an opportunity to learn basic and advanced analysis
performed with AQUA-DUCT.
If you have any questions, do not hesitate to contact me directly or write
an email to info.aquaduct.pl
I'm looking forward to meeting you during the webinar.
All the best
Maria Bzówka
Tunneling Group
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Received on Fri Sep 11 2020 - 06:30:03 PDT
