What?
The workshop will be a one-week event comprising 10 periods (~3 hours each) that include both theory and computer laboratory. It will presented in English and then translated to Spanish. It will be based on a workshop in 2021.
A major change from the previous workshop is that computer laboratories will be run on Google Colab, which is accessible through the internet. The laboratories will be adapted from the 2021 workshop, IIBM3202 Molecular Modeling and Simulation from the Institute for Biological and Engineering at Pontificia Universidad Catolica de Chile, and TeachOpenCADD.
The workshop will be primarily taught by David Minh. Some modules will be taught by guest lecturers: Joseph DePaolo-Boisvert, Kunj Patel, Jennifer Sorescu, Laurentiu Spiridon, Sivanujan Suthaharan. Spiridon is a staff scientist in the Romanian Institute of Biochemistry. The others are Minh’s students and will be presenting under his supervision.
Topics are as follows:
| Day | Period 1 | Period 2 |
|---|---|---|
| 1 | Introductory remarks [key/pdf]. Lab: Introduction to Google Colab [colab]. Fundamentals of biological macromolecules [key/pdf]. Lab: Structural visualization with py3DMol [colab]. Lab: Structural visualization with NGL View (alternative) [colab]. [Recording]. | Three-dimensional models. Structure determination by X-ray crystallography, NMR, and CryoEM (Sorescu) [key/pdf]. Structure prediction [key/pdf]. Lab: Homology modeling with MODELLER [colab]. [Recording]. |
| 2 | Electrostatics and solvation by continuum dielectric models [key/pdf]. Lab: Visualizing protonation and electrostatics [colab]. [Recording]. | Molecular docking (Patel) [key/pdf]. Lab: Molecular docking with AutoDock Vina [colab]. [Recording]. |
| 3 | Molecular mechanics force fields (DePaolo-Boisvert) [key/pdf]. Lab: Preparing a system for molecular simulation [colab]. [Recording]. | Quantum mechanics/molecular mechanics (QM/MM) (Suthaharan) [key/pdf]. Lab: QM/MM analysis of MPro catalysis [colab]. [Recording]. |
| 4 | Molecular simulation (Spiridon). Markov chain Monte Carlo. Molecular dynamics. Constrained dynamics. Integrators, thermostats, and barostats [key/pdf]. Lab: Performing a molecular simulation with Robosample [colab]. [Recording]. | Lab: Performing a molecular simulation with OpenMM [colab]. Lab: Analysis of molecular simulations. Equilibration. Alignment and visualization of trajectories. Root mean square properties. Estimating expectation values. Dimensionality reduction [colab]. Markov State Models. Conformational clustering. Markov chains. Microstates and empirical transition matrices. Computing equilibrium populations and kinetics [key/pdf]. [Recording]. |
| 5 | Simulating and analyzing thermodynamic processes. Thermodynamic processes. Umbrella sampling. Replica exchange. Statistical estimation of expectations and free energies [key/pdf]. Binding free energy calculations (DePaolo-Boisvert). Thermodynamic cycles. Alchemical methods. Quality metrics. Pose prediction [key/pdf]. Lab: YANK health report (DePaolo-Boisvert) [colab]. [Recording]. | Guacherna. To facilitate preparations for Guacherna, there will not be a workshop period . |
Recordings are available as a free online resource.
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 Colombia, Romania, and the United States of America.
Up to 25 students may participate at Simon Bolivar University in Barranquilla, Colombia, and 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 affiliates of Simon Bolivar University and Illinois Tech and individuals working with a workshop instructor or collaborator.
After the workshop, lecture recordings and slides will be made freely available online.
When?
The workshop will be held from March 14 to March 18, 2022. Modules will start at the following times, which are in Colombia Time (COT)/Central Daylight Time (CDT) and Eastern European Time (EST):
| Module | COT/CDT | EST |
|---|---|---|
| 1 | 9 am | 4 pm |
| 2 | 2 pm | 9 pm |
All participants are welcome to work through the modules synchronously. Participants in COT/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.
Where?
The workshop will be held at Simon Bolivar University in Barranquilla, Colombia.
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 Colombia, Romania, and the United States; and
- to provide a rich cultural exchange experience that will foster this collaboration.