The POVME (POcket Volume MEasurer) algorithm has been widely adopted as a simple-to-use tool for measuring and characterizing pocket volumes and shapes. In this lecture, we’ll explore the details of the POVME algorithm.
After the lecture, there will be a hands-on tutorial. The tutorial requires the following programs:
- Python 2.X: https://www.python.org/downloads/
- NumPy and SciPy: http://www.scipy.org/scipylib/download.html
- matplotlib: http://matplotlib.org/downloads.html
- VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Installing the Software on Your Laptop
You’re welcome to install all this software on your laptop, but it can be challenging on some systems. We recommend downloading a prepared VirtualBox image of Ubuntu with everything pre-installed.
- VirtualBox: https://www.virtualbox.org/wiki/Downloads
- Ubuntu OVA file:
Here are detailed instructions describing how to get our version of Ubuntu up and running on your laptop:
Installation instructions for:
Day1 – Identifying flexible pockets and neural network scoring methods (POVME and NNScore)
Day2 – “Developing target focused libraries, hotspot mapping, screening strategies
- Download and install the Oracle VirtualBox platform package for your operating system: https://www.virtualbox.org/wiki/Downloads
a. For Windows, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#installation_windows
b. For Macs, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#idp46856129667856
c. For Linux, detailed instructions can be found here: https://www.virtualbox.org/manual/ch02.html#install-linux-host
Install the Ubuntu virtual machine (VM)
a. Down load Ubuntu_15.014_NBCR.v2.ova: insert link
b. If the VirtualBox program is not running, open it by double clicking on the VirtualBox icon.
c. Select “File” -> “Import appliance”
d. Use the file dialog menu to select Ubuntu_15.014_NBCR.v2.ova and click “Continue”
e. If things have gone well, you should see something like the following:
f. Click “Import” to install the virtual machine.