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About: Molecular Distance Measures

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

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Metadata

Name: Molecular Distance Measures
ID: m11608
Language: English (en)
Summary: Given a set of structures of the same molecule, it is often necessary to decide which are more similar or less similar to each other. This module presents a few ways to approach that problem, including root mean squared distance (RMSD), least RMSD, and intramolecular distance measures.
Subject: Science and Technology
Keywords: dRMSD, intramolecular distance, least RMSD, lRMSD, protein distance, RMSD, structure alignment
Document Type: -//CNX//DTD CNXML 0.5 plus MathML//EN
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), Brian Chen (brianyc@cs.rice.edu)

Latest version: 1.23 (history)
First publication date: Jul 21, 2003 3:42 pm -0500
Last revision to module: Jun 11, 2007 4:52 am -0500

Downloads

PDF: m11608_1.23.pdf PDF file, for viewing content offline and printing. Learn more.
XML: m11608_1.23.cnxml XML that defines the structure and contents of the module, minus any included media files. Can be reimported in the editing interface. Learn more.

Version History

Version: 1.23 Jun 11, 2007 4:52 am -0500 by Hernan Stamati
Changes:
.

Version: 1.22 Jun 11, 2007 4:48 am -0500 by Hernan Stamati
Changes:
.

Version: 1.21 Apr 2, 2007 3:12 pm -0500 by Hernan Stamati
Changes:
Added reference for optimal alignment with matrices.

Version: 1.20 Mar 26, 2007 7:31 pm -0500 by Hernan Stamati
Changes:
Filled in the rotation matrix section.

Version: 1.19 Mar 17, 2007 8:36 pm -0500 by Hernan Stamati
Changes:
Made initial paragraphs consistent with new presentation order.

Version: 1.18 Mar 17, 2007 8:24 pm -0500 by Hernan Stamati
Changes:
Put Matrix method before Quaternion method.

Version: 1.17 Mar 10, 2007 6:46 pm -0600 by Hernan Stamati
Changes:
Added suggested edits.

Version: 1.16 Sep 15, 2006 3:54 pm -0500 by Chuck Bearden
Changes:
Converted JPEG images to PNG to fix PDF printing.

Version: 1.15 May 9, 2006 8:09 pm -0500 by David Schwarz
Changes:
Edited, added references.  Changed roles.

Version: 1.14 May 9, 2006 1:07 pm -0500 by David Schwarz
Changes:
Split module, made some corrections.

Version: 1.13 Apr 26, 2006 5:07 pm -0500 by Brian Chen
Changes:
asdasd

Version: 1.12 Apr 25, 2006 7:49 pm -0500 by Brian Chen
Changes:
more pics ftw.

Version: 1.11 Apr 22, 2006 11:19 pm -0500 by Brian Chen
Changes:
Fixed section tabbing.

Version: 1.10 Apr 22, 2006 11:11 pm -0500 by David Schwarz
Changes:
Brian added local alignment section.

Version: 1.9 Apr 18, 2006 7:05 pm -0500 by Hernan Stamati
Changes:
Added section on Optimal Alignment using matrices.

Version: 1.8 Mar 28, 2006 8:27 pm -0600 by Hernan Stamati
Changes:
Added some proofs.

Version: 1.7 Mar 28, 2006 7:41 pm -0600 by Hernan Stamati
Changes:
Added proofs of quaternion formulas.

Version: 1.6 Mar 28, 2006 6:57 pm -0600 by David Schwarz
Changes:
Replaced with Molecular Distance Measures module.

Version: 1.5 Mar 23, 2006 4:33 pm -0600 by Chuck Bearden
Changes:
Publishing to make new roles effective.

Version: 1.4 Oct 11, 2003 5:31 pm -0500 by (None)
Changes:
modified module

Version: 1.3 Sep 19, 2003 9:31 pm -0500 by Amarda Shehu
Changes:
changed organization and added content

Version: 1.2 Sep 15, 2003 2:08 pm -0500 by Amarda Shehu
Changes:
added brief description of assignments

Version: 1.1 Sep 15, 2003 1:15 pm -0500 by Amarda Shehu
Changes:
just submitting for reference purposes

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American Chemical Society (ACS) Style Guide:

Kavraki, L. Molecular Distance Measures, OpenStax-CNX Web site. http://cnx.org/content/m11608/1.23/, Jun 11, 2007.

American Medical Assocation (AMA) Manual of Style:

Kavraki L. Molecular Distance Measures [OpenStax-CNX Web site]. June 11, 2007. Available at: http://cnx.org/content/m11608/1.23/.

American Psychological Assocation (APA) Publication Manual:

Kavraki, L. (2007, June 11). Molecular Distance Measures. Retrieved from the OpenStax-CNX Web site: http://cnx.org/content/m11608/1.23/

Chicago Manual of Style (Bibliography):

Kavraki, Lydia. "Molecular Distance Measures." OpenStax-CNX. June 11, 2007. http://cnx.org/content/m11608/1.23/.

Chicago Manual of Style (Note):

Lydia Kavraki, "Molecular Distance Measures," OpenStax-CNX, June 11, 2007, http://cnx.org/content/m11608/1.23/.

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

Kavraki, L. 2007. Molecular Distance Measures. OpenStax-CNX, June 11, 2007. http://cnx.org/content/m11608/1.23/.

Modern Languages Association (MLA) Style Manual:

Kavraki, Lydia. Molecular Distance Measures. OpenStax-CNX. 11 June 2007 <http://cnx.org/content/m11608/1.23/>.