User:Eric Martz/Introduction to Structural Bioinformatics 2016: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (25 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: | ||
# 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 145: | Line 156: | ||
The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.) | The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.) | ||
* Use '''Firefox''' (or Safari). The molecule will rotate slowly with jerky jumps in other browsers. Internet Explorer and Edge are especially bad for Jmol. | |||
*Enter your 4-character PDB code at FirstGlance, and you should see the molecule you have chosen. | *Enter your 4-character PDB code at FirstGlance, and you should see the molecule you have chosen. | ||
| Line 180: | 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> | ||
<br><!--http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt--> | <br><!--http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt--> | ||
<span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing | <span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing Example of a Completed Report]</span> (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.) | ||
===Section 1: Identity=== | ===Section 1: Identity=== | ||
| Line 207: | Line 222: | ||
**RNA chains | **RNA chains | ||
:<font color='gray'>Available in the '''molecule information tab''' in FirstGlance: Chain Details. You can identify a residue in any chain by touching it with the mouse (spinning off!). DNA residues are DA, DG, DC, DT while RNA residues are A, G, C and U.</font> | :<font color='gray'>Available in the '''molecule information tab''' in FirstGlance: Chain Details. You can identify a residue in any chain by touching it with the mouse (spinning off!). DNA residues are DA, DG, DC, DT while RNA residues are A, G, C and U.</font> | ||
*Ligands and Non-Standard Residues: Give the | *Ligands and Non-Standard Residues: Give the one to three-letter abbreviations and '''full names''' for all ligands and non-standard residues. If none, so state. ([[Standard residues]]) | ||
:<font color='gray'>The ''molecule information tab'' in FirstGlance lists the 1 to 3-letter abbreviations for each ligand and non-standard residue, and their full names. Click on an abbreviation to locate that entity in the model. See also ''Composition'' in FirstGlance's Views tab. </font> | :<font color='gray'>The ''molecule information tab'' in FirstGlance lists the 1 to 3-letter abbreviations for each ligand and non-standard residue, and their full names. Click on an abbreviation to locate that entity in the model. See also ''Composition'' in FirstGlance's Views tab. </font> | ||
===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 217: | Line 232: | ||
See [[How to see conserved regions]]. | See [[How to see conserved regions]]. | ||
:If Proteopedia lacks a pre-calculated ''Evolutionary Conservation'' for your molecule, and you do your own calculation at the ConSurf Server, be sure to <font color='#d00000'>include the address of the ConSurf result in your | :If Proteopedia lacks a pre-calculated ''Evolutionary Conservation'' for your molecule, and you do your own calculation at the ConSurf Server, be sure to <font color='#d00000'>include the address of the ConSurf result in your report slide!</font>. | ||
===Section 4: Hydrophobic/Polar=== | ===Section 4: Hydrophobic/Polar=== | ||
| Line 223: | Line 238: | ||
===Section 5: Hydrophobic Core=== | ===Section 5: Hydrophobic Core=== | ||
Are there hydrophobic cores in your molecule? For soluble proteins, expect a hydrophobic core in ''[http://proteopedia.org/wiki/index.php/Domain each domain]''. Support your conclusion with a <font color='e000e0'><b>snapshot</b></font>. <font color='gray'>Be sure to use the ''Hydrophobic/Polar'' view from FirstGlance and turn on the ''Slab'' button.</font> | |||
===Section 6: Charge=== | ===Section 6: Charge=== | ||
| Line 258: | Line 273: | ||
The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. <font color="gray">Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why. </font> | The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. <font color="gray">Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why. </font> | ||
In Powerpoint, animations move only when the slides are projected (full-screen). | <!--In Powerpoint, animations move only when the slides are projected (full-screen). | ||
'''Method 1:''' When your Polyview-3D job is done, you will see the animation in the web browser. Simply drag the animation directly from the Polyview-3D web page and drop it into a slide. If the result does not animate when you project the slide, try the following method. | '''Method 1:''' When your Polyview-3D job is done, you will see the animation in the web browser. Simply drag the animation directly from the Polyview-3D web page and drop it into a slide. If the result does not animate when you project the slide, try the following method. | ||
'''Method 2:''': | '''Method 2:''': --> | ||
After your animation is completed and appears in the PolyView-3D web page: | |||
#Right-click (Mac: control-click, or trackpad 2-finger click) on the animation in the Polyview-3D web page, and select Save Image As ... | #Right-click (Mac: control-click, or trackpad 2-finger click) on the animation in the Polyview-3D web page, and select Save Image As ... | ||
#Save the image to the Desktop. | #Save the image to the Desktop. | ||
#Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide. | #Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide. | ||
# | #In Google Slides, the animation should move immediately. | ||
<!--http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt--> | <!--http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt--> | ||
| Line 275: | 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''. | ||
| Line 287: | Line 305: | ||
#Double click the hydrogen bond donor and acceptor atoms to insert a distance monitor. | #Double click the hydrogen bond donor and acceptor atoms to insert a distance monitor. | ||
Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing | Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing '''exactly one hydrogen bond'''. Be sure to identify the two entities (amino acids, nucleotides, ligand) by name, chain, and sequence number. I need enough detail to be able to reproduce what you are reporting. | ||
===Section 11 - How Structure Supports Function=== | ===Section 11 - How Structure Supports Function=== | ||
Write a | Write a brief description ''in your own words'' (avoid plagiarism!) of how the structure of this protein supports its function. Doing some online research will strengthen your description. | ||
Include links to supporting references. Wikipedia can be cited, but authoritative sources, such as peer-reviewed scientific journal articles or government websites, will have more weight. | Include links to supporting references. Wikipedia can be cited, but authoritative sources, such as peer-reviewed scientific journal articles or government websites, will have more weight. | ||
Your description should be at least | Your description should be at least 75 words. More work, if well done, will earn more credit. | ||
Section 11 in the [https://docs.google.com/presentation/d/1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq-dadnA/edit?usp=sharing Sample Report] is longer than the minimum required, but illustrates the sort of thing that could be done if you can spend the time. | |||
==VII. See Also== | ==VII. See Also== | ||
