Physics-based RNA structure prediction

Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic para...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Xu, Xiaojun [verfasserIn] Chen, Shi-Jie

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	RNA Vfold 2D structure prediction 3D structure prediction Tertiary motif

Anmerkung:	© The Author(s) 2015

Übergeordnetes Werk:	Enthalten in: Biophysics reports - Beijing : Institute of Biophysics, Chinese Academy of Sciences, 2015, 1(2015), 1 vom: 09. Juli, Seite 2-13
Übergeordnetes Werk:	volume:1 ; year:2015 ; number:1 ; day:09 ; month:07 ; pages:2-13

Links:	Volltext

DOI / URN:	10.1007/s41048-015-0001-4

Katalog-ID:	SPR038301687

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spelling	10.1007/s41048-015-0001-4 doi (DE-627)SPR038301687 (SPR)s41048-015-0001-4-e DE-627 ger DE-627 rakwb eng Xu, Xiaojun verfasserin aut Physics-based RNA structure prediction 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2015 Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. RNA (dpeaa)DE-He213 Vfold (dpeaa)DE-He213 2D structure prediction (dpeaa)DE-He213 3D structure prediction (dpeaa)DE-He213 Tertiary motif (dpeaa)DE-He213 Chen, Shi-Jie aut Enthalten in Biophysics reports Beijing : Institute of Biophysics, Chinese Academy of Sciences, 2015 1(2015), 1 vom: 09. Juli, Seite 2-13 (DE-627)844073350 (DE-600)2842777-4 2364-3420 nnns volume:1 year:2015 number:1 day:09 month:07 pages:2-13 https://dx.doi.org/10.1007/s41048-015-0001-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 1 2015 1 09 07 2-13
allfields_unstemmed	10.1007/s41048-015-0001-4 doi (DE-627)SPR038301687 (SPR)s41048-015-0001-4-e DE-627 ger DE-627 rakwb eng Xu, Xiaojun verfasserin aut Physics-based RNA structure prediction 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2015 Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. RNA (dpeaa)DE-He213 Vfold (dpeaa)DE-He213 2D structure prediction (dpeaa)DE-He213 3D structure prediction (dpeaa)DE-He213 Tertiary motif (dpeaa)DE-He213 Chen, Shi-Jie aut Enthalten in Biophysics reports Beijing : Institute of Biophysics, Chinese Academy of Sciences, 2015 1(2015), 1 vom: 09. Juli, Seite 2-13 (DE-627)844073350 (DE-600)2842777-4 2364-3420 nnns volume:1 year:2015 number:1 day:09 month:07 pages:2-13 https://dx.doi.org/10.1007/s41048-015-0001-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 1 2015 1 09 07 2-13
allfieldsGer	10.1007/s41048-015-0001-4 doi (DE-627)SPR038301687 (SPR)s41048-015-0001-4-e DE-627 ger DE-627 rakwb eng Xu, Xiaojun verfasserin aut Physics-based RNA structure prediction 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2015 Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. RNA (dpeaa)DE-He213 Vfold (dpeaa)DE-He213 2D structure prediction (dpeaa)DE-He213 3D structure prediction (dpeaa)DE-He213 Tertiary motif (dpeaa)DE-He213 Chen, Shi-Jie aut Enthalten in Biophysics reports Beijing : Institute of Biophysics, Chinese Academy of Sciences, 2015 1(2015), 1 vom: 09. Juli, Seite 2-13 (DE-627)844073350 (DE-600)2842777-4 2364-3420 nnns volume:1 year:2015 number:1 day:09 month:07 pages:2-13 https://dx.doi.org/10.1007/s41048-015-0001-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 1 2015 1 09 07 2-13
allfieldsSound	10.1007/s41048-015-0001-4 doi (DE-627)SPR038301687 (SPR)s41048-015-0001-4-e DE-627 ger DE-627 rakwb eng Xu, Xiaojun verfasserin aut Physics-based RNA structure prediction 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2015 Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. RNA (dpeaa)DE-He213 Vfold (dpeaa)DE-He213 2D structure prediction (dpeaa)DE-He213 3D structure prediction (dpeaa)DE-He213 Tertiary motif (dpeaa)DE-He213 Chen, Shi-Jie aut Enthalten in Biophysics reports Beijing : Institute of Biophysics, Chinese Academy of Sciences, 2015 1(2015), 1 vom: 09. Juli, Seite 2-13 (DE-627)844073350 (DE-600)2842777-4 2364-3420 nnns volume:1 year:2015 number:1 day:09 month:07 pages:2-13 https://dx.doi.org/10.1007/s41048-015-0001-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 1 2015 1 09 07 2-13
language	English
source	Enthalten in Biophysics reports 1(2015), 1 vom: 09. Juli, Seite 2-13 volume:1 year:2015 number:1 day:09 month:07 pages:2-13
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topic_facet	RNA Vfold 2D structure prediction 3D structure prediction Tertiary motif
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author	Xu, Xiaojun
spellingShingle	Xu, Xiaojun misc RNA misc Vfold misc 2D structure prediction misc 3D structure prediction misc Tertiary motif Physics-based RNA structure prediction
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topic_title	Physics-based RNA structure prediction RNA (dpeaa)DE-He213 Vfold (dpeaa)DE-He213 2D structure prediction (dpeaa)DE-He213 3D structure prediction (dpeaa)DE-He213 Tertiary motif (dpeaa)DE-He213
topic	misc RNA misc Vfold misc 2D structure prediction misc 3D structure prediction misc Tertiary motif
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title	Physics-based RNA structure prediction
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title_sort	physics-based rna structure prediction
title_auth	Physics-based RNA structure prediction
abstract	Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. © The Author(s) 2015
abstractGer	Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. © The Author(s) 2015
abstract_unstemmed	Abstract Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions. © The Author(s) 2015
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title_short	Physics-based RNA structure prediction
url	https://dx.doi.org/10.1007/s41048-015-0001-4
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up_date	2024-07-03T17:18:22.268Z
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