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Writing Successful Grant Proposals

12/28/2012

1 Comment

 
Watch this 3-min video by the American Chemical Society for Clue #1 on Writing Science Proposals: Make the Most of Your Project Summary
1 Comment

1-Click Docking

12/19/2012

6 Comments

 
The authors of this app made it possible to draw a molecule online and dock it with simply one click!

http://blog.mcule.com/2012/12/1-click-docking.html


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.

Zoe

6 Comments

Very comprehensive ChemDraw tutorial

12/18/2012

2 Comments

 
2 Comments

How to extract pages from a PDF document to create a new PDF document

12/17/2012

0 Comments

 
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
7. Done!

Zoe

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Comparing Binding Sites with SiteMap

12/12/2012

0 Comments

 
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:
http://www.schrodinger.com/seminarprior/19/38/

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


See also:
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."

Eva


0 Comments

Crossover - Run Windows Applications on Linux

12/12/2012

2 Comments

 
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/

Evi&Zoe
2 Comments

Adding new user to a group in Ubuntu

12/10/2012

0 Comments

 
To create a new user in Ubuntu type:

sudo adduser -ingroup GROUP USERNAME

or

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)

Zoe


0 Comments

Visualize Glide XP scoring function terms with XP Visualizer

12/10/2012

1 Comment

 
Glide XP Visualizer, visualizes Glide XP scoring function terms in Maestro. Its main  functions are:
  • To display the Glide XP results from a pose viewer file (jobname_pv.mae) in a table of XP terms for each ligand.
  • To provide 3D visualizations for XP terms. Information for these visualizations is read from the pose viewer file. The descriptor file (jobname.xpdes), which is also generated by Glide XP, can be used instead; it must be in the same directory as the pose viewer file.
  • To allow selective evaluation of ligands (and groups of ligands) within the table. This helps you analyze ligands separately during the screening process.
Before you can use the Glide XP Visualizer, you must generate the descriptor information. This information is not included in a normal XP run. To generate it, select Write XP descriptor information in the Settings tab of the Ligand Docking panel. You should also select Write pose viewer file in the Output tab of the Ligand Docking panel to write the required pose viewer file.

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.

Eva


1 Comment

ChEMBL resources for drug discovery

12/3/2012

1 Comment

 
  • ChEMBLdb - a drug discovery SAR and bioactivity database.
  • SARfari - a sequence, binding site, structure, SAR integration platform.
  • DrugEBIlity - Drug target annotation & prioritisation.
  • ChEMBL-malaria and ChEMBL-NTD Data repository for neglected tropical diseases.
  • Open Source Intelligence (OSINT), Public-Private partnerships & Precompetitive activities.
1 Comment

    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

    lab group members!

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