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    Education: Training in Molecular Modeling and Molecular Dynamics @ NIH
    Submitted by Vijayaraj Nagarajan; posted on Saturday, February 17, 2018

    March 13-16, 2018
    National Institutes of Health
    9000 Rockville Pike
    Building 60, Room 162
    Bethesda, MD 20892, USA
    events.r20.constantcontact.com/regi[...]c3073

    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 use popular open source tools and techniques necessary for conducting successful molecular modeling and dynamics experiments in the cloud.

    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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