Connexions

Sections
You are here: Home » Content » Geometric Methods in Structural Computational Biology

About: Geometric Methods in Structural Computational Biology

Collection type: Course

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

View content

Metadata

Name: Geometric Methods in Structural Computational Biology
ID: col10344
Language: English (en)
Summary: This course is a short series of lectures on Structural Computational Biology, with an emphasis on geometric algorithms. Topics covered include basic data structures for modeling proteins; kinematics and inverse kinematics of protein chains; distance measures and alignment algorithms for protein structures; motif finding for the functional annotation of proteins; the application of robotics-derived methods to problems in protein modeling; and protein-ligand docking. The development of this course has been supported by NSF 0203396. A number of people have contributed to the development of this course and include (in alphabetical order) Kostas Bekris, Brian Chen, Allison Heath, Mark Moll, Miguel Teodoro, Amarda Shehu, David Schwarz, and Hernan Stamati. The authors are grateful to Jean-Claude Latombe for his help in the initial stages of this project and to the many students who have taken this course at Rice University and have provided useful feedback.
Collection Subtype: Course
Subject: Science and Technology
Keywords: analysis of protein motion, area and volume of proteins, distance measures for proteins, geometric algorithms in biology, geometric methods in structural biology, motif identification in proteins, probablistic roadmap methods, protein classification, protein flexibility, protein functional annotation, protein modeling, robotics methods for protein modeling, structural computational biology
License: Creative Commons Attribution License CC-BY 2.0
Authors: Lydia E. Kavraki (kavraki@rice.edu)
Copyright Holders: Lydia E. Kavraki (kavraki@rice.edu)
Maintainers: Lydia E. Kavraki (kavraki@rice.edu), David Schwarz (dschwarz@rice.edu), Hernan Stamati (hstamati@cs.rice.edu), Amarda Shehu (shehua@cs.rice.edu)
Latest version: 1.6 (history)
First publication date: Mar 22, 2006 11:38 am US/Central
Last revision to collection: Jun 11, 2007 6:32 pm GMT-5
Collection Structure XML: col10344_1.6_collection.xml
All collection files: col10344_1.6_complete.zip

Version History

Version: 1.6 Jun 11, 2007 6:32 pm GMT-5 by Hernan Stamati
Changes: 
Added Dimensionality Reduction module to the index.
Version: 1.5 May 9, 2006 6:37 pm GMT-5 by Lydia E. Kavraki
Changes: 
Added ack section
Version: 1.4 May 9, 2006 6:31 pm GMT-5 by Lydia E. Kavraki
Changes: 
LK added acknowledgments
Version: 1.3 May 9, 2006 3:23 pm GMT-5 by David Schwarz
Changes: 
Added Lydia to author list, added protein classification module.
Version: 1.2 May 8, 2006 1:44 pm GMT-5 by David Schwarz
Changes: 
Added remaining modules and placed assignments in their own folder.
Version: 1.1 Mar 27, 2006 4:19 pm US/Central by David Schwarz
Changes: 
Initial publication, three pages linked:  Lectures 1 and 2, and assignment 1.

How to Reuse and Attribute This Content

If you derive a copy of this content using a Connexions account and publish your version, proper attribution of the original work will be automatically done for you.

If you reuse this work elsewhere, in order to comply with the attribution requirements of the license (CC-BY 2.0), you must include

  • the authors' names: Lydia Kavraki
  • the title of the work: Geometric Methods in Structural Computational Biology
  • the Connexions URL where the work can be found: http://cnx.org/content/col10344/1.6/

See the citation section below for examples you can copy.

How to Cite and Attribute This Content

The following citation styles comply with the attribution requirements for the license (CC-BY 2.0) of this work:

American Chemical Society (ACS) Style Guide:

Kavraki, L. Geometric Methods in Structural Computational Biology, Connexions Web site. http://cnx.org/content/col10344/1.6/, Jun 11, 2007.

American Medical Assocation (AMA) Manual of Style:

Kavraki L. Geometric Methods in Structural Computational Biology [Connexions Web site]. June 11, 2007. Available at: http://cnx.org/content/col10344/1.6/.

American Psychological Assocation (APA) Publication Manual:

Kavraki, L. (2007, June 11). Geometric Methods in Structural Computational Biology. Retrieved from the Connexions Web site: http://cnx.org/content/col10344/1.6/

Chicago Manual of Style (Bibliography):

Kavraki, Lydia. "Geometric Methods in Structural Computational Biology." Connexions. June 11, 2007. http://cnx.org/content/col10344/1.6/.

Chicago Manual of Style (Note):

Lydia Kavraki, "Geometric Methods in Structural Computational Biology," Connexions, June 11, 2007, http://cnx.org/content/col10344/1.6/.

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

Kavraki, L. 2007. Geometric Methods in Structural Computational Biology. Connexions, June 11, 2007. http://cnx.org/content/col10344/1.6/.

Modern Languages Association (MLA) Style Manual:

Kavraki, Lydia. Geometric Methods in Structural Computational Biology. Connexions. 11 June 2007 <http://cnx.org/content/col10344/1.6/>.