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231225s2021 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.26695
|2 doi
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|a pubmed25n1086.xml
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|a DE-627
|b ger
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|e rakwb
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|a eng
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| 100 |
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|a Lubecka, Emilia A
|e verfasserin
|4 aut
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| 245 |
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|a ESCASA
|b Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons
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|c 2021
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Completed 10.01.2022
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|a Date Revised 10.01.2022
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2021 Wiley Periodicals LLC.
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|a A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN ) protons, and the side-chain Hβ protons, given the Cα -trace, have been derived and parameterized, by using the interproton distances calculated from a set of 140 high-resolution non-homologous protein structures. The mean standard deviation over all types of proton pairs in the set was 0.44 Å after fitting. Validation against a set of 41 proteins with NMR-determined structures, which were not considered in parameterization, resulted in average standard deviation from average proton-proton distances of the NMR-determined structures of 0.25 Å, compared to 0.21 Å obtained with the PULCHRA all-atom-chain reconstruction algorithm and to the 0.12 Å standard deviation of the average-structure proton-proton distance of NMR-determined ensembles. The formulas provide analytical forces and can, therefore, be used in coarse-grained molecular dynamics
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a coarse graining
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|a data-assisted molecular modeling
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|a nuclear magnetic resonance
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|a proteins
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|a Proteins
|2 NLM
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|a Liwo, Adam
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 42(2021), 22 vom: 15. Aug., Seite 1579-1589
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnas
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| 773 |
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|g volume:42
|g year:2021
|g number:22
|g day:15
|g month:08
|g pages:1579-1589
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|u http://dx.doi.org/10.1002/jcc.26695
|3 Volltext
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