User:Nikhil Malvankar/IW2018: Difference between revisions

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How to visualize, understand and share/present 3D protein molecular structures

by Nikhil Malvankar, ~~2018~~

by Nikhil Malvankar, 2019

Adapted from Eric Martz

for

for

~~[https:~~/~~/peb.yale.edu/integrated-workshop PEB Integrated Workshop]~~

MB&B 420a/720a Macromolecular Structure Fall 2019

Yale University USA

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*Additional work beyond the minimum required may earn extra credit.

*Due date: ~~TBA~~.

*Due date: 22 October 2018 .

This is not a test. It is to help you learn by doing. Ask for help!

[https://~~docs~~.google.com/~~presentation~~/d/~~1wW1fJfRBfQGXjoS989O5Wz2JuBXVU8LPMlhCq~~-~~dadnA~~/~~edit~~?usp=sharing Example of a Completed Report] (You may import these slides into a new presentation of your own, and use them as a templates, putting in your own content.)

[https://drive.google.com/file/d/1EswWlN_X6qwwrkP7d16mLOR0d4-1fVAN/view?usp=sharing Example of a Completed Report] (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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===Section 3: Evolutionary Conservation===

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])

See [[Introduction to Evolutionary Conservation]].   (Example 4d7b: [http://consurf.tau.ac.il 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 two snapshots illustrating a highly conserved region, and a contrasting region.

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===Section 7: Cation-Pi Interactions===

Use [http://capture.caltech.edu/ CaPTURE] program to identify energetically significant cation-pi interactions within proteins

Show a snapshot 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. The cation-pi interaction tool, and instructions for measuring distances, are in the ''Tools Tab''.

===Section 8: Biological Unit===

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Your description should be at least 75 words. More work, if well done, will earn more credit.

Section 10 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.

Section 10 in the [https://drive.google.com/file/d/1NyNhIJTVhmdNwry6Q3nxucig9x6e5-jx/view?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==

@@ Line 27: / Line 27: @@
 <center>
 <span style="font-size:160%">How to visualize, understand and share/present 3D protein molecular structures</span><br>
-<span style="font-size:130%">by Nikhil Malvankar, 2018
+<span style="font-size:130%">by Nikhil Malvankar, 2019
 <!--<font color="magenta"> DRAFT UNDER REVISION</font>-->
 </span><br>
 Adapted from Eric Martz <br>
-<span style="font-size:115%">for
+<span style="font-size:130%">for
-[https://peb.yale.edu/integrated-workshop PEB Integrated Workshop]</span>
+MB&B 420a/720a Macromolecular Structure Fall 2019</span>
 <br>
 Yale University USA
@@ Line 192: / Line 192: @@
 *Additional work beyond the minimum required may earn extra credit.
-*<font color="red">Due date: TBA.</font>
+*<font color="red">Due date: 22 October 2018 .</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-->
-<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.)
+<span style="font-size:140%;background:#c0ffc0;">[https://drive.google.com/file/d/1EswWlN_X6qwwrkP7d16mLOR0d4-1fVAN/view?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===
@@ Line 224: / Line 224: @@
 ===Section 3: Evolutionary Conservation===
-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])
+See [[Introduction to Evolutionary Conservation]]. &nbsp; (Example 4d7b: [http://consurf.tau.ac.il 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.
@@ Line 243: / Line 243: @@
 ===Section 7: Cation-Pi Interactions===
+Use [http://capture.caltech.edu/ CaPTURE] program to identify energetically significant cation-pi interactions within proteins
 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 8: Biological Unit===
@@ Line 276: / Line 280: @@
 Your description should be at least 75 words. More work, if well done, will earn more credit.
-Section 10 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.
+Section 10 in the [https://drive.google.com/file/d/1NyNhIJTVhmdNwry6Q3nxucig9x6e5-jx/view?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==