Virtual Hands-on Workshop on Computational Biophysics 2020

Virtual Hands-on Workshop on Computational Biophysics 2020

Dates: October 12 - 15, 2020
Application Deadline: September 25 @ 5:00 pm (ET)

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*Due to the associated travel restrictions related to the spread of COVID-19, and to safeguard workshop participants, we have decided to restructure the Hands-on Workshop on Computational Biophysics into a "virtual workshop."  Applicants will be updated with more details soon. We regret the inconvenience for this change and appreciate your patience as we deal with these exceptional circumstances.


This workshop covers a wide range of physical models and computational approaches for the simulation of biological systems at multiple scales, using cutting edge technology including ProDy, NAMDVMD, iGNM and ANM.  The course is based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways and druggability simulations. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers, elastic network models, and steered molecular dynamics simulations.

The workshop will be presented by members of the Theoretical and Computational Biophysics Group ( from the University of Illinois at Urbana-Champaign (UIUC) and the National Center for Multiscale Modeling of Biological Systems (MMBioS) from the University of Pittsburgh.

The workshop is designed for students and researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students set up and run simulations.


  • Elastic Network Models (ENMs) and Collective Motions.
  • Gaussian Network Model (GNM),
  • Anisotropic Network Model (ANM)
  • Introduction to ProDy API and its applications
  • ProDy Analysis of Ensembles of Structures
  • Ensemble analysis using ProDy
  • Evol: Sequence Conservation and Evolution
  • SignDy: Signature Dynamics of Protein Families
  • Computational Studies of Biomolecular Systems with Molecular Dynamics Simulation
  • Molecular Dynamics Simulations with NAMD and VMD
  • Modeling the Dynamics of System & Environment using Elastic Network Models
  • Using VMD QwikMD and NAMD softwares

Workshop Instructors:

Ivet Bahar (University of Pittsburgh)
Emad Tajkhorshid (UIUC)
Pemra Doruker (University of Pittsburgh)

Assistant Instructors:


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