This page describes a workshop in June 2021. For information about more recent or upcoming workshops, go to the home page.
What?
The workshop will be a one-week event comprising 10 periods (~3 hours each) that include both theory and computer laboratory. If you would like to be a formal participant in the workshop, please submit an application.
The workshop will be primarily taught by David Minh with guest lectures from Andrew Howard, Laurentiu Spiridon, and Soohaeng Yoo Willow. Topics are as follows:
| Day | Period 1 | Period 2 |
|---|---|---|
| 1 | Structural visualization [key/pdf]. Fundamentals of biological macromolecules (Howard) [ppt/pdf]. Structure determination (Howard) [ppt/pdf]. Tutorial: Linux terminal basics [key/pdf]. Tutorial: visualization and structural alignment with VMD [key/pdf]. Reference: alternative introduction to biological macromolecules [key/pdf]. | Structure prediction and electrostatics [key/pdf]. Protein structure prediction [key/pdf]. Electrostatics and solvation [key/pdf]. Exercise: visualizing electrostatics [key/pdf]. |
| 2 | Molecular docking and virtual screening [key/pdf]. Molecular docking [key/pdf]. Tutorial: AutoDock Vina [key/pdf]. Virtual screening [key/pdf]. Tour: Virtual screening of FDA-approved drugs against HIV protease [key/pdf]. | Biomolecular potential energy functions (Willow). Molecular mechanics force fields. Mixed quantum mechanics/molecular mechanics [pdf]. |
| 3 | Molecular simulation (Spiridon). Markov chain Monte Carlo. The Metropolis-Hastings Algorithm. Hamiltonian Monte Carlo and molecular dynamics. Constrained dynamics including torsion and rigid-body dynamics. Integrators, thermostats, and barostats [pdf]. Robosample [pdf]. | Analysis of molecular simulations [key/pdf]. Basics: Equilibration. Alignment and visualization of trajectories. Root mean square properties. Estimating expectation values [key/pdf]. Dimensionality reduction with principal components analysis [key/pdf]. |
| 4 | Markov State Models [key/pdf]. Conformational clustering [key/pdf]. Markov chains. Microstates and empirical transition matrices. Computing equilibrium populations and kinetics [key/pdf]. | Simulating and analyzing thermodynamic processes [key/pdf]. Thermodynamic processes. Umbrella sampling. Replica exchange [key/pdf]. Statistical estimation of expectations and free energies [key/pdf]. |
| 5 | Binding free energy calculations . Thermodynamic cycles. Alchemical methods [key/pdf]. | Analysis of alchemical binding free energy calculations . Quality metrics. Pose prediction [key/pdf]. |
Lectures may be recorded and computer laboratory exercises may be posted online for participants to complete asynchronously and as a free online resource.
During the workshop, we will be using the following software:
- Visual Molecular Dynamics (VMD) for visualizing biological macromolecules and molecular dynamics trajectories.
- AutoDock Tools & AutoDock Vina for performing molecular docking.
- Robosample for performing constrained molecular dynamics.
- Anaconda python 3. The Python programming language is widely used in the scientific community. It includes many packages for data analysis and visualization. Anaconda provides a high-quality management of virtual environments. The virtual machine includes the following packages in two conda environments, msmbuilder and analysis (which contains everything else):
- jupyter notebook to create and view documents that contain live code, equations, visualizations, and narrative text.
- matplotlib to create data visualizations.
- OpenMM to perform molecular simulations.
- pySCF to perform quantum chemistry calculations.
- ProDy to analyze protein structural dynamics.
- pymbar, implementing the multistate Bennett acceptance ratio method for estimating expectation values and free energy differences.
- yank for performing alchemical free energy calculations.
- msmbuilder to create statistical models for biomolecular dynamics.
For your convenience, David’s PhD student Jim Tufts has prepared a virtual machine that contains all of this software and a compiled version of Robosampler. To use this virtual machine, you will first need to install Virtual Box. The user name is chemuser and initial password is vm.
We will also use these web servers:
- Homology modelling
- I-TASSER, one of most accurate in competitions
- Swiss Model, one of the fastest
- Advanced Poisson-Boltzmann Solver (APBS) server
Who?
This workshop will introduce advanced undergraduate students, graduate students, and research scientists in chemistry, biology, and related fields to computational methods for modeling biological macromolecules. Workshop participants will mostly be from the United States of America, Romania, and Vietnam.
Up to 15 students may participate as part of a class at the Illinois Institute of Technology: Chem 456, Computational Biochemistry and Drug Design. An additional 25 students may participate online and receive support from the instructors.
Participants should have a laptop computer capable of running the virtual machine.
If you would like to be a formal participant in the workshop, please submit an application. Formal participants will be able to attend the workshop live and participate in live discussions. Priority for formal participation will be given to Illinois Tech students and individuals working with a workshop instructor or collaborator.
After the workshop, lecture recordings and slides may posted online.
When?
The workshop will be held from June 28 to July 2, 2021. Modules will start at the following times, which are in Central Daylight Time (CDT), Eastern European Standard Time (EEST), and Indochina Time (ICT):
| Module | CST | EEST | ICT |
|---|---|---|---|
| 1 | 9 am | 5 pm | 9 pm |
| 2 | 1 pm | 9 pm | 1 am (+1 d) |
All participants are welcome to work through the modules synchronously. Participants in CDT are especially encouraged to participate live. However, it will probably make sense for remote participants, based on their time zone, to complete modules at a more convenient time. All participants can reach out to all workshop instructors for online office hours. Online office hours will be held at the following times:
Workshop instructors will hold online office hours at the following times:
| Instructor | CDT | EEST | ICT |
|---|---|---|---|
| David | 7 pm | 3 am (+1 d) | 7 am (+1 d) |
| Laurentiu | 1 am | 9 am | 1 pm |
| Soohaeng | 8 am | 4 pm | 8 pm |
Where?
The workshop will be held on the Illinois Tech campus in Wishnick Hall 210.
Why?
The purpose of this workshop will be
- to further the education of workshop participants in the field of computational biochemistry;
- to promote international scientific collaboration, especially between the United States, Vietnam, and Romania