User:Eric Martz/Introduction to Structural Bioinformatics 2016: Difference between revisions

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-<!-- NOTES FOR 2016:
+<!-- NOTES FROM 2016:
+For 2017:
+Some people had no catpi so give them an alternative.
+: chains in the asymmetric unit to be clear. And suggest cartoon so each chain has a different color.
+: 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"
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 <span style="font-size:160%">How to visualize, understand and share/present 3D protein molecular structures</span><br>
 <span style="font-size:130%">by Eric Martz, 2016
-<font color="magenta"> DRAFT UNDER REVISION</font></span>
+<!--<font color="magenta"> DRAFT UNDER REVISION</font>-->
-<br>
+</span><br>
 <span style="font-size:115%">for
 [https://www.micro.umass.edu/courses/catalog/microbio-497l-advanced-microbiology-lab-techniques Microbiology 497L: Advanced Microbiology Lab Techniques]</span>
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 . Learn how ''FirstGlance in Jmol'' makes it easy to see structure-function relationships in the protein you chose.
-. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be a Powerpoint file emailed to emartz@microbio.umass.edu. You will not present your report in class.)
+. Write a report including snapshots of your protein that illustrate your answers to the questions below. (Your report will be in the form of [http://slides.google.com Google Slides] emailed to emartz@microbio.umass.edu. You will not present your report in class.)
 ==III. Protein Structure and Structural Bioinformatics==
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 |}
+{| align="right"
+|-
+|
+[https://docs.google.com/presentation/d/1lS59hde5F6ur9VCBO1_eHwXbhQcUHByPPVi12w6PSRM/edit?usp=sharing '''SLIDESHOW''']
+<imagemap>
+Image:Protein-structure-4-levels-I-flat.png|300 px|
+default [http://proteopedia.org/wiki/images/f/f3/Protein-structure-4-levels-I-flat.png]
+</imagemap>
+<hr>
+|-
+|
+<imagemap>
+Image:Protein-structure-4-levels-III-flat.png|300 px|
+default [http://proteopedia.org/wiki/images/6/6e/Protein-structure-4-levels-III-flat.png]
+</imagemap>
+|}
 :<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span>
 ::A. [http://www.umass.edu/molvis/workshop/allstruc/whycare.htm Why do we care] about protein 3D structure?
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 **<u>Report the PDB code you chose to the instructor</u> to make sure it is not already taken.
 **It must have protein.
-**It will be more interesting if it contains some non-protein: DNA, RNA or ligand.
+**It will be more interesting if it contains some non-protein: ligand, or DNA or RNA.
 **X-ray results should have resolution of 3 &Aring; or better.
 *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://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].
 # Random PDB Entry in Proteopedia (see ''Random'' at top left of this page in the ''navigation'' box).
-# Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure.
+# Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure. See also [[Practical Guide to Homology Modeling]] which includes instructions for finding empirical 3D models for a protein sequence.
 ==V. Explore Your Molecule==
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 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.
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 FirstGlance does NOT use '''[[Java]]''' unless you tell it to. Using Java will make larger proteins load faster, rotate more smoothly, and change views quicker.  Use '''Firefox or Internet Explorer''' (or Safari) for Java. Chrome and Edge do not support Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the ''Preferences'' tab in FirstGlance. See [[Installing and enabling Java]].
 </ul></ul>
-Here are two Views in  FirstGlance that will be used in your Powerpoint report:
+Here are two Views in  FirstGlance that will be used in your report:
 ====A. Hydrophobic/Polar====
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 *Large, protruding hydrophobic surface areas (>25 &Aring; in their smaller diameter) may indicate transmembrane proteins (insoluble). Examples:
 **[http://firstglance.jmol.org/fg.htm?mol=7ahl 7ahl]
+**showing [http://opm.phar.umich.edu/protein.php?pdbid=7ahl bilayer boundaries] (click on "Jmol"; ligand toggles boundaries).
 **[http://firstglance.jmol.org/fg.htm?mol=1bl8 1bl8]
-**showing [http://opm.phar.umich.edu/protein.php?pdbid=1r3j bilayer boundaries] (click on "Jmol"; ligand toggles boundaries).
 **[[Gramicidin Channel in Lipid Bilayer]].
@@ Line 152: / Line 182: @@
 ==VI. Report Slides==
-Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''] (recommended), Powerpoint or Libre Office Impress. To start Powerpoint, click Spotlight ([[Image:Spotlight-icon.png]] upper right corner of screen), enter "powerpoint" and it will appear on the taskbar at the bottom of the screen. Click there to start it.
+Answer the questions below in slides, using [http://slides.google.com '''Google Slides'''].
+*Name your report '''YourLastName-497L''', for example <font color='red'><b>Sandler-497L</b></font>. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report to '''emartz@microbio.umass.edu''' for grading.
+::(While viewing your report slides, click the blue <i>Share</i> button at the upper right, then <i>Get shareable link</i>, and paste the link into the email.)
+:You will ''not'' be asked to present your report in class.
+*Each slide MUST be labeled at the top with its section number, e.g. ''Section 1''.
-Name your report '''yourLastName-497L''', for example <font color='red'><b>sandler-497L.pptx</b></font>. ''If the name of your report does not begin with your family name, you will lose 2 points.'' When completed, email a link to your report (or attach a Powerpoint or Libre Office file) to '''emartz@microbio.umass.edu''' for grading. You will ''not'' be asked to present your report in class.
+*Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
-Each slide MUST be labeled at the top with its section number, e.g. ''Section 1''.
+*Additional work beyond the minimum required may earn extra credit.
-Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
+*<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>
-<br>
+<br><!--http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt-->
-<span style="font-size:140%;background:#c0ffc0;">[http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt Sample Completed Powerpoint Assignment]</span> (You may download it, rename the file, and use it as a template.)
+<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===
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 **DNA 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 3-letter abbreviations and '''full names''' for all ligands and non-standard residues. If none, so state. ([[Standard residues]])
+*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>
 ===Section 3: Evolutionary Conservation===
-See [[Introduction to Evolutionary Conservation]]. &nbsp; ([http://firstglance.jmol.org/fg.htm?mol=http%3A//bioinformatics.org/molvis/pdb/4d7b_consurf1454623073_pipe.pdb 4d7b])
+See [[Introduction to Evolutionary Conservation]]. &nbsp; (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 a <font color='e000e0'><b>snapshot</b></font> illustrating a highly conserved (or variable) 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.
 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 Powerpoint slide!</font>.
+: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===
 Do you think your molecule is water soluble? 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 in a snapshot. Optionally, you may show other views in other snapshots.</font>
-===Section 4A: Hydrophobic Core===
+===Section 5: Hydrophobic Core===
-Is there a hydrophobic core in your molecule? 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>
+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 5: Charge===
+===Section 6: Charge===
-Are there any areas on the surface of your molecule with only positive (or negative) charges? Show <font color='e000e0'><b>snapshots</b></font> illustrating your conclusions.  <font color='gray'>Be sure to use the ''Charge'' view from FirstGlance in a snapshot.</font>
+Are there any areas on the surface of your molecule with only positive (or negative) charges? Show <font color='e000e0'><b>snapshots</b></font> illustrating your conclusions.  <font color='gray'>Be sure to use the ''Charge'' view from FirstGlance in your snapshots.</font>
-===Section 5A: Cation-Pi Interactions===
+===Section 7: Cation-Pi Interactions===
 Show a <font color='e000e0'><b>snapshot</b></font> of an energetically significant [[Cation-pi_interactions|cation-pi interaction]]. Include a distance monitor in your snapshot. Also paste in the report from CaPTURE confirming its energetic significance. <font color='gray'>The cation-pi interaction tool, and instructions for measuring distances, are in the ''Tools Tab''.</font>
-===Section 6: Biological Unit===
+===Section 8: Biological Unit===
 In FirstGlance, in the ''molecule information tab'' click ''Biological Unit''. (It is also in the ''Resources Tab''.)
@@ Line 219: / Line 255: @@
 Show side-by-side <font color='e000e0'><b>two snapshots</b></font> comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.
-===Section 7: Animation from Polyview-3D===
+===Section 9: Animation from Polyview-3D===
 Minimal steps to make an animation:
 <!--
@@ Line 237: / 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>
-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 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 ...
 #Save the image to the Desktop.
 #Drag the image file (filename ending in .gif) from the Desktop and drop it into a slide.
-#The animation may not move until the slide is projected.
+#In Google Slides, the animation should move immediately.
-<span style="font-size:140%;background:#c0ffc0;">[http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt Powerpoint Slides with Polyview-3D Animations]</span> (These slides are only to show you what is possible. These are not in your assignment.)
+<!--http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt-->
+<span style="font-size:140%;background:#c0ffc0;">[https://docs.google.com/presentation/d/1PAzssvqDRBKFIl9DWvWpXXxM--gtIIdT0p8fMCXfE10/edit?usp=sharing Examples of Slides with Polyview-3D Animations]</span> (These slides are only to show you what is possible. These are not in your assignment.)
 ----
-===Section 8 - 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.
 #Change target selection to ''Residues/Groups''.
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 #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 a hydrogen bond.
+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===
+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.
+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==