Help:Teaching with Proteopedia: Difference between revisions
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Every page in Proteopedia that is titled with a 4-character [[PDB code]] has a link to [[FirstGlance in Jmol]]. ''FirstGlance'' makes it easy to explore the molecular structure in more detail. ''FirstGlance'' reports the number of chains of protein, DNA, RNA, and lists all ligands and non-standard residues with their full names. You can click on any of these to find them. Sequences can be displayed and short sequences can be found. With one click each you can see secondary structure, amino and carboxyl termini, hydrophobic cores (two clicks, one to slice through the center with "Slab"), positive and negative charges, and much more. Tools locate disulfide bonds, salt bridges, cation-pi interactions, and non covalent bonds to any moiety you specify. Help and color keys appear automatically. | Every page in Proteopedia that is titled with a 4-character [[PDB code]] has a link to [[FirstGlance in Jmol]]. ''FirstGlance'' makes it easy to explore the molecular structure in more detail. ''FirstGlance'' reports the number of chains of protein, DNA, RNA, and lists all ligands and non-standard residues with their full names. You can click on any of these to find them. Sequences can be displayed and short sequences can be found. With one click each you can see secondary structure, amino and carboxyl termini, hydrophobic cores (two clicks, one to slice through the center with "Slab"), positive and negative charges, and much more. Tools locate disulfide bonds, salt bridges, cation-pi interactions, and non covalent bonds to any moiety you specify. Help and color keys appear automatically. | ||
When students are given a worksheet or an assignment of suitable questions, ''FirstGlance'' provides an easy way to discover answers. [https://www.umass.edu/molvis/workshop/challeng/2015/ppslides.htm Here are 20 questions] assigned to M.S. students in a [http://workshops.molviz.org 5-day workshop]. These questions apply to any protein; each student chose a different protein to investigate (for example from the [http://atlas.molviz.org Atlas of Macromolecules]. | When students are given a worksheet or an assignment of suitable questions, ''FirstGlance'' provides an easy way to discover answers. | ||
* [[User:Eric Martz/Introduction to Structural Bioinformatics 2016|Here are 11 questions]] for upper level bio-science major undergraduates taking three 3-hour lab sessions. | |||
*[https://www.umass.edu/molvis/workshop/challeng/2015/ppslides.htm Here are 20 questions] assigned to M.S. students in a [http://workshops.molviz.org 5-day workshop]. | |||
*These questions apply to any protein; each student chose a different protein to investigate (for example from the [http://atlas.molviz.org Atlas of Macromolecules]. | |||
Jaswal, O'Hara, Williamson and Springer (2013)<ref>PMID: 24019219</ref> describe in detail how they use ''Proteopedia'', ''FirstGlance in Jmol'' and student-authored presentations about their structure-function analysis projects in a one-semester biochemistry course at Amherst College (Amherst, Massachusetts, USA). | Jaswal, O'Hara, Williamson and Springer (2013)<ref>PMID: 24019219</ref> describe in detail how they use ''Proteopedia'', ''FirstGlance in Jmol'' and student-authored presentations about their structure-function analysis projects in a one-semester biochemistry course at Amherst College (Amherst, Massachusetts, USA). | ||