Advanced Molecular Dynamics

Protein-Ligand Binding (Modes, Affinity, Kinetics)

Structure refinement and related topics

Fundamentals and demo on protein structure refinement, dynamics and conformation search by MD simulations and AlphaFold using ChimeraX.

Intro to Macromolecular Simulation - See original tutorial materials here: <a href="https://bioinformatics.niaid.nih.gov/cmm/maxent">Intro to the Maximum Entropy Method</a> and <a href="https://bioinformatics.niaid.nih.gov/cmm/intro_simulation/">Intro to MacroMolecular Simulation</a>.

Tutorial on using Chimera X for AlphaFold Protein Structure. It starts by showing how search and navigate the database PDB for relevant structural data.

Demo of use of Chimera to analyze protein structure - Part I & II

This training focus on protein folding methods. It starts describing prediction of primary and secondary structure. The instructor introduces Rosetta for folding.

This training helps to provide an introduction to using HPC, the file structure, submitting and monitoring jobs

Training on structural modeling with examples of relevant software such as Phyre and I-Tasser.

Training on structural modeling with demonstration on using the software Modeller.

Lecture on computational drug design. Topics include: denovo ligand design, structure file formats, practical aspects of docking. It shows a hands-on exercise on docking.

Training on function prediction using various algorithms and databases. It goes into details of using multiple blast parameters and it leverages databases on protein interaction.

Step by step guide on using Chimera to study mutations in protein structure. It explains parameters and options to choose when using the tool.

Demo of Chimera for learning how to create a movie using chimera to highlight various aspects of a protein stucture.

This is an introductory session to teach the basics of Unix, working with Shell, file manipulation and other basic tasks.

Structure Prediction using Rosetta

Practical training on using tools from the MEME suite to find and analyze sequence motifs.

Practical training on using tools from the MEME suite to find and analyze sequence motifs.

Practical excercises on using Chimera for preparing a morph and movie

Introductory training as preparation for python programming. Topics include using the terminal, the linux file directory structure, and basic commands for file manipulation.

Introductory training on protein docking. Topics include methods, evaluation criteria and a hands on exercise on assembling protein complexes.

Illustration using Visual Molecular Dynamics (VMD)