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

Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein

Research output: Contribution to journalArticle

114 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)D296-301
JournalNucleic acids research
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006

ASJC Scopus subject areas

  • Genetics

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    Flores, S., Echols, N., Milburn, D., Hespenheide, B., Keating, K., Lu, J., Wells, S., Yu, E. Z., Thorpe, M., & Gerstein, M. (2006). The Database of Macromolecular Motions: new features added at the decade mark. Nucleic acids research, 34(Database issue), D296-301.