NDLI: UMass Morph Server: Macromolecular Dynamics Analyses Using Elastic Network Models

Content Provider	IEEE Xplore Digital Library
Author	Yunho Jang Kim, M.K.
Copyright Year	2005
Description	Author affiliation: Dept. of Mech. & Ind. Eng., Massachusetts Univ., Amherst, MA (Yunho Jang; Kim, M.K.)
Abstract	The geometry-based mechanical models called elastic network models (ENMs) in various resolutions have been developed for the study of macromolecular motions. In a coarse-grained ENM, a biological system is represented as a network of springs connecting representative points. They range from single atoms to functional domains depending on the level of details in modeling. In this paper presented are the various kinds of coarse-graining methods such as symmetry-constrained, rigid-cluster, and hybrid ENMs. They enable us to overcome the computational burden and memory limitation in the conventional molecular dynamics (MD) simulations and full-atom normal mode analysis (NMA) without loss of generality. For the broad impact of this work on the structural biology area we also develop the UMass Morph Server (UMMS). Based on the requests from online users, UMMS does not only serve a harmonic NMA that describes thermal behaviors (i.e., fluctuations) of a macromolecule around its equilibrium state, but also generates anharmonic transition pathways between two end conformations by using the elastic network interpolation (ENI) also developed by the author. In addition, UMMS can provide two unique features as follows: (i) interpretation of massive MD data by finding essential pathways (ii) the conformation prediction incorporated with time-resolved information such as FRET data. Many example movies and numeric data can be downloadable at http://biomechanics.ecs.umass.edu/umms.html
Starting Page	2599
Ending Page	2602
File Size	343086
Page Count	4
File Format	PDF
ISBN	0780387414
DOI	10.1109/IEMBS.2005.1617001
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-01-17
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Network servers Biological system modeling Solid modeling Biological systems Springs Joining processes Biology computing Computational modeling Analytical models Fluctuations
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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