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USA

Training in Molecular Modeling and Molecular Dynamics

February 18-21,2020


Where?

National Institutes of Health

9000 Rockville Pike

Building 60, Room 162

Bethesda, MD 20892, USA


Objectives

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

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.

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

Highlights

  • Cloud-based, high performance computing platform
  • Training provided by active NIH researchers
  • Cookbook style bound manual for all exercises
  • Continuing Education Credits

For more information and registration, please visit the following page;

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