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About: Assignment 1: Visualization and Ranking of Protein Conformations

Module by: Lydia E. Kavraki. E-mail the author

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Name: Assignment 1: Visualization and Ranking of Protein Conformations
ID: m11615
Language: English (en)
Summary: This assigment introduces students to the visualization software VMD and allows them to get familiar with protein structures. Students are required to visualize protein conformations and understand the differences between structures based on their geometry. Students will rank the provided conformations based on their geometric differences.
Subject: Science and Technology
Keywords: collision, conformation, crd, energy, pdb, secondary structure, steric, Van der Waals, VMD
License: Creative Commons Attribution License CC-BY 1.0
Authors: Lydia E. Kavraki (kavraki@rice.edu)
Copyright Holders: Lydia E. Kavraki (kavraki@rice.edu)
Maintainers: Lydia E. Kavraki (kavraki@rice.edu), Amarda Shehu (shehua@cs.rice.edu), David Schwarz (dschwarz@rice.edu), Hernan Stamati (hstamati@cs.rice.edu), Drew Bryant (dbryant@rice.edu)
Latest version: 1.22 (history)
First publication date: Sep 23, 2003 8:01 pm GMT-5
Last revision to module: Mar 17, 2009 2:08 am GMT-5
Module XML: m11615_1.22.cnxml

Version History

Version: 1.22 Mar 17, 2009 2:08 am GMT-5 by Lydia E. Kavraki
Changes: 
added new section on protein catalytic sites.
Version: 1.21 Apr 12, 2007 12:02 pm GMT-5 by Hernan Stamati
Changes: 
Added instructions to increase the buffer size in VMD's tk console.
Version: 1.20 Apr 10, 2007 3:55 pm GMT-5 by Hernan Stamati
Changes: 
Clarified Q3.
Version: 1.19 Apr 10, 2007 12:37 am GMT-5 by Hernan Stamati
Changes: 
Included a version of the tcl script that computes RMSD that prints to a file, with the module files. Linked to it from the assignment.
Version: 1.18 Apr 3, 2007 2:57 pm GMT-5 by Hernan Stamati
Changes: 
Added a sentence to explain how to write to a file within a tcl script.
Version: 1.17 Mar 14, 2007 5:53 pm GMT-5 by Hernan Stamati
Changes: 
Updated descriptions, links, and assignment files to be consistent.
Version: 1.16 May 9, 2006 8:06 pm GMT-5 by David Schwarz
Changes: 
Roles changed.
Version: 1.15 Mar 28, 2006 10:27 pm US/Central by Hernan Stamati
Changes: 
None.
Version: 1.14 Mar 28, 2006 9:36 pm US/Central by David Schwarz
Changes: 
minor corrections
Version: 1.13 Mar 28, 2006 1:56 pm US/Central by Hernan Stamati
Changes: 
Fixed some links.
Version: 1.12 Mar 28, 2006 1:43 pm US/Central by Hernan Stamati
Changes: 
Fixes.
Version: 1.11 Mar 28, 2006 12:20 pm US/Central by Hernan Stamati
Changes: 
Added appendix on installing VMD.
Version: 1.10 Mar 28, 2006 11:35 am US/Central by David Schwarz
Changes: 
Link to HIV 1 protease trajectory fixed.
Version: 1.9 Mar 28, 2006 11:33 am US/Central by David Schwarz
Changes: 
Added HIV 1 protease MD simulation file to files, and made a link to it.
Version: 1.8 Mar 28, 2006 11:14 am US/Central by David Schwarz
Changes: 
Removed due date.

Linked files correctly.
Version: 1.7 Mar 28, 2006 2:46 am US/Central by David Schwarz
Changes: 
Fixed or removed links that went to Amarda's directory.
Version: 1.6 Mar 28, 2006 2:39 am US/Central by David Schwarz
Changes: 
Removed reference to Protein Explorer.  Added files for use in assignment as a .zip archive.
Version: 1.5 Mar 27, 2006 4:09 pm US/Central by David Schwarz
Changes: 
Added Hernan to maintainers.
Version: 1.4 Mar 24, 2006 3:04 pm US/Central by David Schwarz
Changes: 
This module has been changed from an introduction to visualization software into an assignment to get students used to visualization software.
Version: 1.3 Mar 23, 2006 4:30 pm US/Central by Chuck Bearden
Changes: 
Publishing to make new roles effective.
Version: 1.2 Sep 23, 2003 9:15 pm GMT-5 by Amarda Shehu
Changes: 
added para
Version: 1.1 Sep 23, 2003 9:10 pm GMT-5 by Amarda Shehu
Changes: 
created module

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American Chemical Society (ACS) Style Guide:

Kavraki, L. Assignment 1: Visualization and Ranking of Protein Conformations, Connexions Web site. http://cnx.org/content/m11615/1.22/, Mar 17, 2009.

American Medical Assocation (AMA) Manual of Style:

Kavraki L. Assignment 1: Visualization and Ranking of Protein Conformations [Connexions Web site]. March 17, 2009. Available at: http://cnx.org/content/m11615/1.22/.

American Psychological Assocation (APA) Publication Manual:

Kavraki, L. (2009, March 17). Assignment 1: Visualization and Ranking of Protein Conformations. Retrieved from the Connexions Web site: http://cnx.org/content/m11615/1.22/

Chicago Manual of Style (Bibliography):

Kavraki, Lydia. "Assignment 1: Visualization and Ranking of Protein Conformations." Connexions. March 17, 2009. http://cnx.org/content/m11615/1.22/.

Chicago Manual of Style (Note):

Lydia Kavraki, "Assignment 1: Visualization and Ranking of Protein Conformations," Connexions, March 17, 2009, http://cnx.org/content/m11615/1.22/.

Chicago Manual of Style (Reference, in Author-Date style):

Kavraki, L. 2009. Assignment 1: Visualization and Ranking of Protein Conformations. Connexions, March 17, 2009. http://cnx.org/content/m11615/1.22/.

Modern Languages Association (MLA) Style Manual:

Kavraki, Lydia. Assignment 1: Visualization and Ranking of Protein Conformations. Connexions. 17 Mar. 2009 <http://cnx.org/content/m11615/1.22/>.