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dc.contributor.authorChen, M.
Lin, X.
Lu, W.
Onuchic, J.
Wolynes, P.G.
dc.date.accessioned 2017-02-22T21:07:15Z
dc.date.available 2017-02-22T21:07:15Z
dc.date.issued 2016
dc.identifier.citation Chen, M., Lin, X., Lu, W., et al.. "Protein Folding and Structure Prediction from the Ground Up II: AWSEM for a/ß Proteins." Journal of Physical Chemistry B, (2016) American Chemical Society: http://dx.doi.org/10.1021/acs.jpcb.6b09347.
dc.identifier.urihttps://hdl.handle.net/1911/93962
dc.description.abstract The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For α helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of α/β proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure prediction and makes the free energy profile more funneled toward native configurations. We explore the use of clustering analyses as a way of evaluating the confidence in various structure prediction models. Clustering using a local relative order parameter (mutual Q) of the predicted structural ensemble turns out to be optimal. The tightest cluster according to mutual Q generally has the most correctly folded structure. Since there is no bioinformatic input, AAWSEM amounts to an ab initio protein structure prediction method that combines the efficiency of coarse-grained simulations with the local structural accuracy that can be achieved from all-atom simulations.
dc.language.iso eng
dc.publisher American Chemical Society
dc.rights Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
dc.title Protein Folding and Structure Prediction from the Ground Up II: AWSEM for a/ß Proteins
dc.type Journal article
dc.citation.journalTitle Journal of Physical Chemistry B
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1021/acs.jpcb.6b09347
dc.type.publication publisher version
local.sword.agent Converis


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