Geometric simulation of flexible motion in proteins

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)

Abstract

This chapter describes the use of physically simplified analysis and simulation methods – pebble-game rigidity analysis, coarse-grained elastic network modeling, and template-based geometric simulation – to explore flexible motion in protein structures. Substantial amplitudes of flexible motion can be explored rapidly in an all-atom model, retaining realistic covalent bonding, steric exclusion, and a user-defined network of noncovalent polar and hydrophobic interactions, using desktop computing resources. Detailed instructions are given for simulations using FIRST/FRODA software installed on a UNIX/Linux workstation. Other implementations of similar methods exist, particularly NMSim and FRODAN, and are available online. Topics covered include rigidity analysis and constraints, geometric simulation of flexible motion, targeting between known structures, and exploration of motion along normal mode eigenvectors.
Original languageEnglish
Title of host publicationProtein Dynamics
Subtitle of host publicationMethods and Protocols
EditorsDennis R. Livesay
Place of PublicationNew York
PublisherHumana Press
Pages173-192
VolumeII
ISBN (Print)9781627036573
DOIs
Publication statusPublished - 30 Sep 2013

Publication series

NameMethods in Molecular Biology.
PublisherSpringer
Volume1084

Fingerprint

Rigidity
Proteins
UNIX
Computer workstations
Eigenvalues and eigenfunctions
Atoms
Linux

Cite this

Wells, S. A. (2013). Geometric simulation of flexible motion in proteins. In D. R. Livesay (Ed.), Protein Dynamics: Methods and Protocols (Vol. II, pp. 173-192). (Methods in Molecular Biology.; Vol. 1084). New York: Humana Press. https://doi.org/10.1007/978-1-62703-658-0_10

Geometric simulation of flexible motion in proteins. / Wells, Stephen A.

Protein Dynamics: Methods and Protocols. ed. / Dennis R. Livesay. Vol. II New York : Humana Press, 2013. p. 173-192 (Methods in Molecular Biology.; Vol. 1084).

Research output: Chapter in Book/Report/Conference proceedingChapter

Wells, SA 2013, Geometric simulation of flexible motion in proteins. in DR Livesay (ed.), Protein Dynamics: Methods and Protocols. vol. II, Methods in Molecular Biology., vol. 1084, Humana Press, New York, pp. 173-192. https://doi.org/10.1007/978-1-62703-658-0_10
Wells SA. Geometric simulation of flexible motion in proteins. In Livesay DR, editor, Protein Dynamics: Methods and Protocols. Vol. II. New York: Humana Press. 2013. p. 173-192. (Methods in Molecular Biology.). https://doi.org/10.1007/978-1-62703-658-0_10
Wells, Stephen A. / Geometric simulation of flexible motion in proteins. Protein Dynamics: Methods and Protocols. editor / Dennis R. Livesay. Vol. II New York : Humana Press, 2013. pp. 173-192 (Methods in Molecular Biology.).
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