User:Eric Martz/Introduction to Structural Bioinformatics I, 2014: Difference between revisions
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Section 2: "1-3 character" | |||
Sec 8: Start with "show me ONE hydrogen bond". Describe which atoms participate in the hydrogen bond, including their residue names and sequence number. If you show more than one distance, indicate which bond you are describing. I need enough detail to be able to reproduce what you are reporting. | |||
Renumber sections to enumerate inline 4A and 5A. | |||
Consider adding exptl vs full length sequence lengths and alignment. | |||
Hydrophobic core: mention "per domain". Cf. 1acc. | |||
If students have problems or get stuck, they should contact the TA. If the TA cannot confidently answer the question, TA should contact me (give cell phone). | |||
In 2014, 3 people picked 1mbo, so have them register and avoid dups! | |||
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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:160%">How to visualize, understand and share/present 3D protein molecular structures</span><br> | ||
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Image:1000px-Amino Acids.svg.png|200 px| | Image:1000px-Amino Acids.svg.png|200 px| | ||
default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png] | default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png] | ||
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:<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | :<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | ||
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<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> | <br> | ||
<span style="font-size:140%;background:#c0ffc0;">[http://bioinformatics.org/molvis/ppt/martz-565- | <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.) | ||
===Section 1: Identity=== | ===Section 1: Identity=== | ||
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===Section 4: Hydrophobic/Polar=== | ===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> | 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=== | |||
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> | |||
===Section 5: Charge=== | ===Section 5: 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 a snapshot.</font> | ||
===Section 5A: 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 6: Biological Unit=== | ||
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#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''. | ||
#Click on something small to select it as a "target", such as a ligand, or a single amino acid. | #Click on something small to select it as a "target", such as a ligand, or a single amino acid. Choose an amino acid with an uncharged polar side chain, such as Ser, Thr, Asn, Gln, Tyr, His. | ||
#Click the link to ''Show atoms contacting target''. | #Click the link to ''Show atoms contacting target''. | ||
#Click ''Center contacts''. | #Click ''Center contacts''. | ||
#Uncheck ''Backbones''. | #Uncheck ''Backbones''. | ||
#Click the 4th thumbnail image [[Image:Contact4.gif]] to display the contacts as balls and sticks colored by element. The element color key is at the bottom of the Contacts help panel in FirstGlance. | |||
#Zoom in (and click ''Return to Contacts'' if necessary). | #Zoom in (and click ''Return to Contacts'' if necessary). | ||
#Uncheck all categories of non-covalent bonds. | #Uncheck all categories of non-covalent bonds. | ||
