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BACKGROUND

Predicting the effect of a mutation on the structure and function of a protein is not just for researchers with super-computer facilities. Thanks to public cloud computing options, anyone with basic molecular biology background can setup and run compute intensive computational modeling and dynamics experiments.

OBJECTIVES

Participants will get a brief hands-on introduction to the R platform, followed by hands-on walkthrough for creating several different popular plots, graphs and maps. We will start from formatting data and go all the way to loading data, setting parameters, creating the images and saving the outputs.

Hands-on Skills/Tools Taught:

Ab initio protein structure modeling: QUARK / Rosetta
Remote homology detection: HHpred
Fragment-based protein structure modeling: Phyre2
Homology-based protein structure modeling: I-TASSER, MODELLER
Protein structure quality analysis: PROCHECK, WHAT_IF, Verify3D, PDB-REDO
Protein structure refinement: ModRefiner, ModLoop, Ramachandran plot
Macromolecular visualization: VMD, USCF Chimera
Molecular dynamics: NAMD

Discussion forums: Education: Training in Molecular Modeling and Molecular Dynamics at NIH

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