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@article{Greener:2017:10.1016/j.str.2017.01.008,
author = {Greener, JG and Filippis, I and Sternberg, MJE},
doi = {10.1016/j.str.2017.01.008},
journal = {Structure},
pages = {546--558},
title = {Predicting protein dynamics and allostery using multi-protein atomic distance constraints},
url = {http://dx.doi.org/10.1016/j.str.2017.01.008},
volume = {25},
year = {2017}
}

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TY  - JOUR
AB  - The related concepts of protein dynamics,  conformational ensembles and allostery are of-ten difficult to study with molecular dynamics (MD) due to the timescales involved.   Wepresent ExProSE (Exploration of Protein Structural Ensembles), a distance geometry-basedmethod that generates an ensemble of protein structures from two input structures. ExProSEprovides a unified framework for the exploration of protein structure and dynamics in a fastand accessible way. Using a dataset of apo/holo pairs it is shown that existing coarse-grainedmethods can often not span large conformational changes. For T4-lysozyme ExProSE is ableto generate ensembles that are more native-like than tCONCOORD and NMSim, and com-parable to targeted MD. By adding additional constraints representing potential modulators,ExProSE can predict allosteric sites. ExProSE ranks an allosteric pocket first or second for 27out of 58 allosteric proteins, which is similar and complementary to existing methods.  TheExProSE source code is freely-available.
AU  - Greener,JG
AU  - Filippis,I
AU  - Sternberg,MJE
DO  - 10.1016/j.str.2017.01.008
EP  - 558
PY  - 2017///
SN  - 1878-4186
SP  - 546
TI  - Predicting protein dynamics and allostery using multi-protein atomic distance constraints
T2  - Structure
UR  - http://dx.doi.org/10.1016/j.str.2017.01.008
UR  - http://hdl.handle.net/10044/1/43553
VL  - 25
ER  -

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