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How to efficiently change background color with GIMP

9/18/2014

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This tutorial shows you how you can efficiently replace the background of an image with another in GIMP, through the use of the color to alpha plug-in, which is very effective in selecting the image from the backgroung.

1.
The first step is to activate the color to alpha plug-in. Its menu location is <image> Filters -> Colors -> Color To Alpha, where <image> means to right click on the image. If its grayed-out, it means that you have an indexed image. If its not there, upgrade your gimp to 1.2.x.

2.
Next use the Color Picker Tool to select the background color. Or just open the toolbox (Tool -> Toolbox) and choose the background color from the last image. Then choose Layer -> Create New Layer, and choose "Foreground color".

3. (Optional)
When you used the color picker to select the background, a window with the color popped up. Click, hold, and drag from the color portion of this window to the color portion of the Color To Alpha plug-in. If using Gimp for Windows, you'll have to right-click on the destination button and select the Foreground - drag n' drop doesn't work. Click OK after the color indicator on the Color To Alpha plug-in is changed to blue. Alternatively, make sure that the "color to alpha" is selected when you did Step 1.

4.
Now create a New Layer as a Background. The background will now come on top of your image, but don't worry because your image is just layered beneath. Choose "Layer -> Stack -> Reverse Layer Order".

5. Remove the layers: Image -> Flatten.

6. If you want to change your image resolution, do:
Image>Print_ Size>Set_Image_Print_Resolution.

(tutorial written according to this link)
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Free Virtual Symposium: Advances in Drug Discovery and DevelopmentĀ 

9/17/2014

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On September 24, 2014, a world-class group of scientists from biotech, pharma and academia will present the latest research findings and new technologies that are driving the design, discovery and development of new drugs – from small molecules and monoclonals to RNA therapeutics and gene-editing technologies.

The event is free and organized by the American Chemical Society (ACS) and ACS's magazine C&EN news.

To register for free please follow this link.  Even if you can’t make the live lectures or the time zone is not convenient for you, all presentations will be archived and available on demand for three months.

You will even have the chance to “Walk the floor” in a virtual exhibition hall, participate in panel discussions and Q&A sessions and do live-chat with peers and vendors.

Some of the talks that I find interesting:

Accurate Prediction of Ligand Binding Free Energies - MARK MURCKO, PhD (Disruptive Biomedical LLC)

Design of Protein Structures, Functions and Assemblies - DAVID BAKER, PhD (HHMI/Univ of Washington)

Site-directed ligand discovery for cryptic sites - MICHELLE ARKIN PhD (UCSF)

The Promises and Challenges of Next-Generation Therapeutics - GREG VERDINE, PhD (Warp Drive Bio)

Structure based Drug Design: G-protein coupled receptors using StaR tech - FIONA MARSHALL (Heptares)

Drug Repositioning in the Era of Personalized Medicine - CRAIG WEBB, PhD (NuMedii)

Panel Discussion:The Business of Biotech - LUKE TIMMERMAN, MATT HERPER, MANDY JACKSON

Exploiting cell death for drug discovery - BRENT STOCKWELL, PhD (HHMI/Columbia University)

The VCNDD: CNS Drug Discovery in Academia - CRAIG W. LINDSLEY, PhD (Vanderbilt Center - VCNDD)

Targeting Lysine Acetylation in Cancer - JAY BRADNER, MD (Dana Farber Cancer Institute)


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Fragment-based docking with CHARMM

9/1/2014

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Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design

Yuri Pevzner , Emilie Frugier , Vinushka Schalk , Amedeo Caflisch , and H. Lee Woodcock
J. Chem. Inf. Model., Just Accepted Manuscript

Abstract
Web-based front end interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), allows researcher to take advantage of the functionality of the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multi-scale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly on the CHARMMing Web server or on local HPC resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-docking's" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

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

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