User:Eric Martz/Introduction to Structural Bioinformatics 2016: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (9 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
<!-- NOTES | <!-- NOTES FROM 2016: | ||
For 2017: | |||
Some people had no catpi so give them an alternative. | |||
2: chains in the asymmetric unit to be clear. And suggest cartoon so each chain has a different color. | |||
10: Be sure to say what kind of bond you are describing, for example "hydrogen bond". | |||
Show them where the link to the abstract is. Ask them to read it an use information learned there in their reports. | |||
Insist that they do their own consurf jobs. The patterns in Ppda consurfDB are not very believable. Probably too many protein functions included. | |||
------------ | |||
Section 2: "1-3 character" | Section 2: "1-3 character" | ||
| Line 134: | Line 145: | ||
**X-ray results should have resolution of 3 Å or better. | **X-ray results should have resolution of 3 Å or better. | ||
*Here are some ways to find a protein with known structure: | *Here are some ways to find a protein with known structure: | ||
# '''Recommended:''' Atlas of Macromolecules ([http://atlas.molviz.org Atlas.MolviZ.Org]). Choose a "Straightforward" or "Challenging" (not "Enormous") molecule that has protein and ligand. | # '''Recommended:''' <span style="font-size:150%;">Atlas of Macromolecules ([http://atlas.molviz.org Atlas.MolviZ.Org]).</span> Choose a "Straightforward" or "Challenging" (not "Enormous") molecule that has protein and ligand. | ||
# [http://pdb101.rcsb.org/motm/motm-by-category Molecule of the Month] at the PDB. Look for PDB codes in the article, and use [http://firstglance.jmol.org FirstGlance] to view them. | # [http://pdb101.rcsb.org/motm/motm-by-category Molecule of the Month] at the PDB. Look for PDB codes in the article, and use [http://firstglance.jmol.org FirstGlance] to view them. | ||
# [http://proteopedia.org/wiki/index.php/Topic_pages Topic Pages] in Proteopedia, or its [http://proteopedia.org/wiki/index.php/Table_of_Contents Table of Contents]. | # [http://proteopedia.org/wiki/index.php/Topic_pages Topic Pages] in Proteopedia, or its [http://proteopedia.org/wiki/index.php/Table_of_Contents Table of Contents]. | ||
| Line 182: | Line 193: | ||
*Additional work beyond the minimum required may earn extra credit. | *Additional work beyond the minimum required may earn extra credit. | ||
*<font color="red">Due date: midnight Thursday March 3.</font> | |||
<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font> | <font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font> | ||
| Line 213: | Line 226: | ||
===Section 3: Evolutionary Conservation=== | ===Section 3: Evolutionary Conservation=== | ||
See [[Introduction to Evolutionary Conservation]]. ([http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/pdb/4d7b_consurf1454623073_pipe.pdb | See [[Introduction to Evolutionary Conservation]]. (Example 4d7b: [http://consurf.tau.ac.il/results/1454623073/output_with_form.php ConSurf], [http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/atlas/pdb/4d7b_consurf1454623073_pipe.pdb Result]) | ||
Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region. | Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show <font color='e000e0'><b>two snapshots</b></font> illustrating a highly conserved region, and a contrasting region. | ||
| Line 279: | Line 292: | ||
===Section 10 - Contacts/Non-covalent Bonds=== | ===Section 10 - Contacts/Non-covalent Bonds=== | ||
Example: [http://firstglance.jmol.org/fg.htm?mol=4d7b 4d7b]. | |||
#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance. | #Click ''Contacts'' in the ''Tools Tab'' in FirstGlance. | ||
#Change target selection to ''Residues/Groups''. | #Change target selection to ''Residues/Groups''. | ||