Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D296-D301; doi:10.1093/nar/gkj046
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (881K) Freely available
Right arrow Screen PDF (265K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Flores, S.
Right arrow Articles by Gerstein, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Flores, S.
Right arrow Articles by Gerstein, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2006, Vol. 34, Database issue D296-D301
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The Database of Macromolecular Motions: new features added at the decade mark

Samuel Flores1,3, Nathaniel Echols2, Duncan Milburn3, Brandon Hespenheide6, Kevin Keating4, Jason Lu3, Stephen Wells6, Eric Z. Yu3, Michael Thorpe6,7 and Mark Gerstein3,4,5,*

1Department of Physics, Yale University P.O. Box 208120, New Haven, CT 06520-8120, USA 2Department of Molecular and Cell Biology, University of California Berkeley, CA 94720, USA 3Molecular Biophysics and Biochemistry Department Bass 432A, 266 Whitney Avenue Yale University New Haven, CT 06520, USA 4Computational Biology and Bioinformatics Program Bass 432A, 266 Whitney Avenue Yale University New Haven, CT 06520, USA 5Department of Computer Science Bass 432A, 266 Whitney Avenue Yale University New Haven, CT 06520, USA 6Center for Biological Physics, Department of Physics and Astronomy, Arizona State University Tempe, AZ 85287, USA 7Department of Chemistry and Biochemistry, Arizona State University Tempe, AZ 85287, USA

*To whom correspondence should be addressed. Tel: +1 203 432 6105; Fax: +1 360 838 7861; Email: Mark.Gerstein{at}yale.edu.

Received August 15, 2005. Revised October 4, 2005. Accepted October 4, 2005.

The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered on MolMovDB. In particular, we further developed the Morph Server to produce improved interpolations between two submitted structures. We added support for multiple chains to the original adiabatic mapping interpolation, allowing the analysis of subunit motions. We also added the option of using FRODA interpolation, which allows for more complex pathways, potentially overcoming steric barriers. We added an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility. We developed tools to relate such points of flexibility in a structure to particular key residue positions, i.e. active sites or highly conserved positions. Lastly, we began relating our motion classification scheme to function using descriptions from the Gene Ontology Consortium.

Correspondence may also be addressed to Samuel Flores. Tel: +1 203 747 2682; Email: Samuel.Flores{at}yale.edu


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 RNAHome page
M. Sharma, G. Bulusu, and A. Mitra
MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch
RNA, September 1, 2009; 15(9): 1673 - 1692.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. Hamdane, C. Xia, S.-C. Im, H. Zhang, J.-J. P. Kim, and L. Waskell
Structure and Function of an NADPH-Cytochrome P450 Oxidoreductase in an Open Conformation Capable of Reducing Cytochrome P450
J. Biol. Chem., April 24, 2009; 284(17): 11374 - 11384.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K.-i. Okazaki and S. Takada
Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
PNAS, August 12, 2008; 105(32): 11182 - 11187.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. A. Hanson, K. Duderstadt, L. P. Watkins, S. Bhattacharyya, J. Brokaw, J.-W. Chu, and H. Yang
Illuminating the mechanistic roles of enzyme conformational dynamics
PNAS, November 13, 2007; 104(46): 18055 - 18060.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J.-B. Jomain, E. Tallet, I. Broutin, S. Hoos, J. van Agthoven, A. Ducruix, P. A. Kelly, B. B. Kragelund, P. England, and V. Goffin
Structural and Thermodynamic Bases for the Design of Pure Prolactin Receptor Antagonists: X-RAY STRUCTURE OF Del1-9-G129R-hPRL
J. Biol. Chem., November 9, 2007; 282(45): 33118 - 33131.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Alazard, L. Mourey, C. Ebel, P. V. Konarev, M. V. Petoukhov, D. I. Svergun, and M. Erard
Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets
Nucleic Acids Res., July 26, 2007; 35(13): 4420 - 4432.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Autin and P. Tuffery
PMG: online generation of high-quality molecular pictures and storyboarded animations
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W483 - W488.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Franklin, P. Koehl, S. Doniach, and M. Delarue
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W477 - W482.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. E. C. Burba, U. Lehnert, E. Z. Yu, and M. Gerstein
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
Bioinformatics, November 15, 2006; 22(22): 2735 - 2738.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.