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==Related papers:== | ==Related papers:== | ||
*SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167. [http://papers.gersteinlab.org/e-print/HingeAtlas/preprint.pdf full text] | *SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167. [http://papers.gersteinlab.org/e-print/HingeAtlas/preprint.pdf full text] | ||
| + | *[http://papers.gersteinlab.org/papers/molmovdb2/ Echols, Milburn, and Gerstein (2003).] Nucleic Acids Res. 31:478-82. | ||
| + | *M Gerstein, A Lesk, C Chothia (1994). "Structural Mechanisms for Domain Movements in Proteins," Biochemistry 33: 6739-6749. (the basis for the original database) | ||
| + | *M Gerstein, R Jansen, T Johnson, J Tsai & W Krebs (1999). "Studying Macromolecular Motions in a Database Framework: from Structure to Sequence," Rigidity theory and applications (ed. M F Thorpe & P M Duxbury, Kluwer Academic/Plenum Publishers), pp. 401-442. [http://papers.gersteinlab.org/papers/rigidity-conf/ full text] (a review article describing protein motions) | ||
| + | *WG Krebs, J Tsai, V Alexandrov, N Echols, J Junker, R Jansen and M Gerstein (2001), "Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping this onto Sequences," Methods in Enzymology (in press). [http://papers.gersteinlab.org/e-print/mots-mie/ full text] (practical discussion of computational analysis of protein motions) | ||
| + | *WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48: 682-95. [http://papers.gersteinlab.org/papers/nmodes/ full text] (in-depth analysis of large set of morphs) | ||
| + | |||
| + | ==Open source and publicly available software used== | ||
| + | This web server and many of the services it provides use [ http://apache.org/ Apache], [http://www.novell.com/linux/ Linux (SUSE)], and [http://www.mysql.com/ mySQL]. The HingeMaster and FlexOracle hinge predictors use [http://dasher.wustl.edu/tinker/ TINKER],[http://www.gromacs.org/ GROMACS], and [http://foldx.crg.es/ FoldX], in addition to software mentioned elsewhere. | ||
| + | |||
| + | ==Support== | ||
| + | The NSF is acknowledged for support (award [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=9723182 DBI-9723182]). | ||
Revision as of 01:11, 23 May 2008
Molecular Movements Database Help and Information Page
The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits. The HingeMaster server predicts hinges in single protein structures using the FlexOracle, hNMb, TLSMD, StoneHinge, and other algorithms.
Contents |
Copyright Statement
Unless otherwise notated, all pages in this database are copyright 1995-2003, Mark Gerstein, all rights reserved. In particular, please do not incorporate this database into other databases without prior permission of the author. Some of our algorithms, notably the HingeMaster and Conformation Explorer, have pending patents. Please use the citation below when refering to the database in print.
Citation Info:
- The citation for the FlexOracle hinge predictor is SC Flores, MB Gerstein (2007). BMC Bioinformatics 8: 215.
- The current citation for the morph server (which explains the CNS and FRODA multi-chain morph engines and other new features) is Flores, Echols, Milburn, Hespenheide, Keating, Lu, Wells, Yu, Thorpe, Gerstein (2006). Nucleic Acids Res. 34:D296-301.
- The citation for the single-chain Morph Server is Krebs and Gerstein (2000). Nucleic Acids Res. 28:1665-75. If you reproduce movies from our site, please cite both of the above articles.
- The original publication of the database was Gerstein and Krebs (1998). Nucleic Acids Res. 26:4280-90.
- If you use our movies in PowerPoint, etc., please cite us as "The Yale Morph Server (http://molmovdb.org)". For any of the newer color movies, you should also cite the [ http://pymol.sourceforge.net/ PYMOL] molecular graphics system.
- If you use the FRODA-LITE option on our morph server, please cite Wells S., Menor S., Hespenheide B.M and Thorpe M.F. (2005) Constrained Geometric Simulation of Diffusive Motion in Proteins. Physical Biology 2, S127-S136. More information and services related to FIRST/FRODA are available at Flexweb.
- If your work makes use of the Catalytic Site Atlas gallery on our movie.cgi page, or the 'Highlight active sites' button on our morph.cgi page, please cite Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton (2004) Nucleic Acids Res. 32(Database Issue):D129-133.
Related papers:
- SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167. full text
- Echols, Milburn, and Gerstein (2003). Nucleic Acids Res. 31:478-82.
- M Gerstein, A Lesk, C Chothia (1994). "Structural Mechanisms for Domain Movements in Proteins," Biochemistry 33: 6739-6749. (the basis for the original database)
- M Gerstein, R Jansen, T Johnson, J Tsai & W Krebs (1999). "Studying Macromolecular Motions in a Database Framework: from Structure to Sequence," Rigidity theory and applications (ed. M F Thorpe & P M Duxbury, Kluwer Academic/Plenum Publishers), pp. 401-442. full text (a review article describing protein motions)
- WG Krebs, J Tsai, V Alexandrov, N Echols, J Junker, R Jansen and M Gerstein (2001), "Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping this onto Sequences," Methods in Enzymology (in press). full text (practical discussion of computational analysis of protein motions)
- WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48: 682-95. full text (in-depth analysis of large set of morphs)
==Open source and publicly available software used==
This web server and many of the services it provides use [ http://apache.org/ Apache], Linux (SUSE), and mySQL. The HingeMaster and FlexOracle hinge predictors use TINKER,GROMACS, and FoldX, in addition to software mentioned elsewhere.
Support
The NSF is acknowledged for support (award DBI-9723182).
