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dc.contributor.authorNoel, Jeffrey K.
Whitford, Paul C.
Onuchic, José N.
dc.date.accessioned 2015-01-06T15:49:13Z
dc.date.available 2015-01-06T15:49:13Z
dc.date.issued 2012
dc.identifier.citation Noel, Jeffrey K., Whitford, Paul C. and Onuchic, José N.. "The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function." The Journal of Physical Chemistry B, 116, no. 29 (2012) American Chemical Society: 8692-8702. http://dx.doi.org/10.1021/jp300852d.
dc.identifier.urihttps://hdl.handle.net/1911/78888
dc.description.abstract Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called “Shadow”. The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.
dc.language.iso eng
dc.publisher American Chemical Society
dc.rights This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
dc.title The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function
dc.type Journal article
dc.contributor.funder National Science Foundation
dc.contributor.funder Cancer Prevention and Research Institute of Texas
dc.contributor.funder National Institutes of Health
dc.citation.journalTitle The Journal of Physical Chemistry B
dc.contributor.org Center for Theoretical Biological Physics
dc.citation.volumeNumber 116
dc.citation.issueNumber 29
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1021/jp300852d
dc.identifier.pmcid PMC3406251
dc.identifier.pmid 22536820
dc.identifier.grantID PHY-0822283 (National Science Foundation)
dc.identifier.grantID MCB-1214457 (National Science Foundation)
dc.identifier.grantID TGMCB110021 (National Science Foundation)
dc.identifier.grantID T32 GM08326 (National Institutes of Health)
dc.type.publication post-print
dc.citation.firstpage 8692
dc.citation.lastpage 8702


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