Computational Biophysics Workshop - Pittsburgh, May 30 - June 2, 2017

Computing labs will be set up for use during the workshop. However, those wishing to bring their own laptop for use in the workshop can follow the instructions below to have it set up for the event. Read into the starting sections of each tutorial to see required software and files.

I. Install Software

Tutorial sessions use the VMD - version 1.9.3, NAMD - version 2.12, and ProDy software packages, plus plotting programs (e.g., Excel on Windows, XMGrace on Unix/Mac) and text editors (e.g, Notepad on Windows, nedit on Unix, TextEdit on Mac) as described on the laptop requirements page. Some tutorials suggest additional software programs (read introductory sections of tutorials). Be sure that all your software is installed and tested before you arrive at the workshop - there is no time on site for installation troubleshooting.

II. Install Tutorials Texts and Files

Each tutorial consists of a text in pdf format, and computer files used in the tutorial. Be sure that you have the files you need each day of the tutorial sessions in place before you arrive at the workshop. Files by day of workshop tutorial session are listed below. It is easiest to follow the tutorials if files are placed in a 'Workshop' directory on the desktop.

Day 1: Collective Dynamics of Proteins Using Elastic Network Models. From single molecules to biological assemblies - Ivet Bahar

Day 2: Bridging Sequence, Structure and Function, and Experiments and Computations. Druggability Simulations - Ivet Bahar - Ivet Bahar

  • The instructions for installing Prody.
    1. Install anaconda python from: http://continuum.io/downloads#all - for Windows machine, install Windows 32-bin anaconda - Python 2.7 - installer. - for mac and linux, you are very likely to have a 64-bit machine, so install the 64-bit python 2.7 version.
    It will install in a standard folder, which is fine. it will change the bash profile so that if you type: python, it should tell you that you are using anaconda python.

    2. For mac/linux, get Biopython by typing:
    pip install -U biopython
    For windows, first get/install VC compiler from here: http://www.microsoft.com/en-us/download/details.aspx?id=44266 before you type:
    pip install -U biopython
    in a command window.

    3. For mac/linux, do this:
    pip install -U ProDy
    on Mac it may ask you to install XCode first before installing ProDy for gcc. say yes. Note, XCode takes about 5-10 min to install.
    For windows, install Prody with the exe installation package.
    http://pypi.python.org/packages/2.7/P/ProDy/ProDy-1.5.1.win32-py2.7.exe


  • ProDy Tutorial
  • NMWiz Tutorial
  • ENM Analysis
  • Ensemble Analysis
  • Structure Analysis
  • Trajectory Analysis
  • Conformational Sampling

  • See also the main tutorial page

Day 3 - Introduction to Protein Structure and Dynamics - Emad Tajkhorshid

Day 4: Statistical Mechanics of Proteins - Emad Tajkhorshid

or

or

Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website during the workshop.