Education: Training in Molecular Modeling and Molecular Dynamics at NIH - Bioinformatics.org

[Next-Generation Sequencing Book]

Vijayaraj Nagarajan • October 27, 2016
Education: Training in Molecular Modeling and Molecular Dynamics at NIH
Nov 29 - Dec 2, 2016
National Institutes of Health
9000 Rockville Pike
Bethesda, MD, USA
http://events.r20.constantcontact.com/register/event?oeidk=a07edct1t5ba9bb92c4&llr=k4uamblab

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

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