![]() (1) Know how to visualize and manipulate protein structures from the Protein Data Bank (PDB) using the VMD software. Students completing these four sessions were able to: To visualize and analyze proteins structures, students learned the VMD program.įour classes, each 75 minutes (among 14 classes of a whole semester) 3D visualization increases student’s comprehension of the link between a biomolecule structure and its functional roleįirst year graduate students and motivated undergraduate studentsīME 468 / PHP 468 – Introduction to Structure and Analysis of Biomolecules (Spring 2019)Ī series of lectures in BME468 introduced students to the principles of protein & DNA structure and function, fundamental principles of protein folding, DNA structures, the spatial and conceptual relationships of biomolecules, role of mutations, the structure of biomolecules in relation to their functions and dysfunctions – which may be linked directly to human diseases. The key advantage of 3D printing is the ability to reproduce very complex protein structures with extreme precision at scale by reading STL files derived from PDB structures using the VMD program. James Alkins).ģD printer services at the Rettner Fabrication Studio were used to print the 3D structure of selected biomolecules using durable materials. ![]() This tool allows students to connect a protein’s sequence and folding domains with the interaction of specific amino acid residues and the protein’s function also, to relate disease-associated mutations with protein misfolding and their potential abnormal-functions.ģD printer at the Rettner Fabrication Studio in Rettner Hall (Mr. Using VMD students can open files from the Protein Data Bank (PDB) containing the structure of different biomolecules and analyze them. It is also a tool to view and analyze the results of molecular dynamic simulations. ![]() VMD is an open-source program designed for modeling, visualization and analysis of biological molecules such as proteins, nucleic acids, etc. Teaching Students to Explore Protein Structures Using the Visual Molecular Dynamics (VMD) program and 3D Printing. University of Rochester, River Campus Libraries University of Rochester, Biomedical Engineering, Pharmacology and Physiology, Center for Musculoskeletal Research
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