During the previous year and a half, I used MidasPlus software to render crystal and NMR structures in the Protein Data Bank, along with other structures not listed in the data base, representing a broad spectrum of macromolecules involved in intermediary metabolism, gene regulation and cell cycle control. The key feature of this exercise is that all renderings are made with a consistent color palette and orientations of related structures are matched. This adds a continuity for students introduced to macromolecular structure for the first time. Reference information contained in PDB header files along with internet addresses for the Protein Data Base and molecular viewing software (like MidasPlus and RASMOL) are provided in the CD-ROM so that, ideally, students will be able to access, view and manipulate the structures represented in the CD. I have contacted representatives at the Brookhaven Protein Data Base and they agree that approaches like this will aid their efforts for outreach to primary educators. Additionally, I have used LEAP molecular model building software (a supplement to AMBER molecular dynamics simulation software) to build a comprehensive library of intermediary metabolites. A continuity of structures ranging from atmospheric O2, CO2 and N2 to nucleotides, carbohydrates, amino acids and fatty acids have been assembled. I am saving these files in both LEAP and PDB file formats and am making these available to the UCSF Computer Graphics Laboratory for distribution. I am using MidasPlus to render these models in the same manner as previously described. Hopefully, scientists that want to model dynamics of metabolites will be able to use these basic models as templates and also update the library with the results of more refined modeling efforts. Students could also access this library and manipulate the models with the previously mentioned viewing software. In the future, as the library is updated with refined models and classrooms are equipped with more powerful computers, students may be able to use molecular dynamics simulators, in conjunction with professional scientific advisors, to quicken advances in this field and add excitement to the learning experience.
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