Watch this 3-min video by the American Chemical Society for Clue #1 on Writing Science Proposals: Make the Most of Your Project Summary
The authors of this app made it possible to draw a molecule online and dock it with simply one click!
The app uses the Autodock Vina software for docking.
Check out also the mcule.com site for more drug discovery tools and a compound database.
1. Open the pdf file
2. File -> Print
3. Select the pages you want to save from your pdf file
4. Select print to file instead of the printer
5. Provide a filename
6. Click Print
When looking for diversity in protein structures, the volume-based or the shape-based analysis of a binding side through SiteMap is more meaningful than looking at the RMSD metric alone, as mentioned in a recent protein preparation Schrodinger webinar by Dr Woody Sherman, which can be found here:
To evaluate protein structure diversity with SiteMap you can perform the following steps:
1. Run SiteMap on each structure -- Computes shape of binding pocket for each structure
3.Generate pairwise volume overlap matrix with the Python script from Script Center "trajectory_binding_site_volumes.py"
4.Perform hierarchical clustering to get diverse binding sites with "volume_cluster.py"
5. Choose desired structures
Halgren T (2007) Chem Biol Drug Des 69(2):146 title: "New method for fast and accurate binding-site identification and analysis."
Halgren T (2009) J Chem Inf Model 49:377 title: "Identifying and characterizing binding sites and assessing druggability."
CrossOver allows you to install many popular Windows applications and PC games on your Linux computer.
It's the best software we have found so far that actually works.
You can try it for free here: http://www.codeweavers.com/products/#cxlinux/
To create a new user in Ubuntu type:
sudo adduser -ingroup GROUP USERNAME
sudo adduser USERNAME
(adds the user and asks you questions about the user)
sudo usermod -G GROUP USERNAME
(changes the primary group of a user, set it to 'lab')
sudo passwd USERNAME
(sets the password of the new user, which should be changed upon first login)
sudo chown -R USERNAME:GROUP /home/USERNAME/
(recursively sets the ownership of the files of the user to GROUP)
Glide XP Visualizer, visualizes Glide XP scoring function terms in Maestro. Its main functions are:
If you forgot to check the 'Write XP descriptor information' option and have results of a long XP job and don't want to rerun it in order to generate the descriptors, you could run an XP job on your previous results with the "Ligand sampling" option set to "None (score in place only)". This will re-score the ligands (and add XP descriptors if you've selected that option), which is much faster than re-docking the ligands.
Christina, Dora, Giannis, Lefteris, Michalis, Sofia, Alexis, Zoe
lab group members!
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