Education: Training in Molecular Modeling and Molecular Dynamics @ NIH

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
https://events.r20.constantcontact.com/register/eventReg?llr=k4uamblab&oeidk=a07ee86owxac41c3073

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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