247 related articles for article (PubMed ID: 35705644)
1. Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.
Shimizu M; Okuda A; Morishima K; Inoue R; Sato N; Yunoki Y; Urade R; Sugiyama M
Sci Rep; 2022 Jun; 12(1):9970. PubMed ID: 35705644
[TBL] [Abstract][Full Text] [Related]
2. Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data.
Ekimoto T; Ikeguchi M
Adv Exp Med Biol; 2018; 1105():237-258. PubMed ID: 30617833
[TBL] [Abstract][Full Text] [Related]
3. Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.
Paissoni C; Jussupow A; Camilloni C
J Chem Theory Comput; 2020 Apr; 16(4):2825-2834. PubMed ID: 32119546
[TBL] [Abstract][Full Text] [Related]
4. Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution.
Larsen AH; Wang Y; Bottaro S; Grudinin S; Arleth L; Lindorff-Larsen K
PLoS Comput Biol; 2020 Apr; 16(4):e1007870. PubMed ID: 32339173
[TBL] [Abstract][Full Text] [Related]
5. Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations.
Thomasen FE; Cuneo MJ; Mittag T; Lindorff-Larsen K
Elife; 2023 Mar; 12():. PubMed ID: 36856266
[TBL] [Abstract][Full Text] [Related]
6. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles.
Chan-Yao-Chong M; Durand D; Ha-Duong T
J Chem Inf Model; 2019 May; 59(5):1743-1758. PubMed ID: 30840442
[TBL] [Abstract][Full Text] [Related]
7. Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.
Ballabio F; Paissoni C; Bollati M; de Rosa M; Capelli R; Camilloni C
J Chem Theory Comput; 2023 Nov; 19(22):8401-8413. PubMed ID: 37923304
[TBL] [Abstract][Full Text] [Related]
8. Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations.
Liu G; Ekmen E; Jalalypour F; Mertens HDT; Jeffries CM; Svergun D; Atilgan AR; Atilgan C; Sayers Z
J Chem Phys; 2023 Feb; 158(8):085101. PubMed ID: 36859088
[TBL] [Abstract][Full Text] [Related]
9. Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD).
Yaacob N; Kamonsutthipaijit N; Soontaranon S; Leow TC; Rahman RNZRA; Ali MSM
Int J Biol Macromol; 2022 Nov; 220():1095-1103. PubMed ID: 36029961
[TBL] [Abstract][Full Text] [Related]
10. Conformational states of Zika virus non-structural protein 3 determined by molecular dynamics simulations with small-angle X-Ray scattering data.
Zhu G; Pan A; Grüber G; Lu L
Prog Biophys Mol Biol; 2019 May; 143():13-19. PubMed ID: 30291845
[TBL] [Abstract][Full Text] [Related]
11. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations.
Bowerman S; Rana ASJB; Rice A; Pham GH; Strieter ER; Wereszczynski J
J Chem Theory Comput; 2017 Jun; 13(6):2418-2429. PubMed ID: 28482663
[TBL] [Abstract][Full Text] [Related]
12. Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data.
Latham AP; Zhang B
J Phys Chem B; 2019 Feb; 123(5):1026-1034. PubMed ID: 30620594
[TBL] [Abstract][Full Text] [Related]
13. Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation.
Okuda A; Shimizu M; Morishima K; Inoue R; Sato N; Urade R; Sugiyama M
Sci Rep; 2021 Mar; 11(1):5655. PubMed ID: 33707747
[TBL] [Abstract][Full Text] [Related]
14. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations.
Chen PC; Shevchuk R; Strnad FM; Lorenz C; Karge L; Gilles R; Stadler AM; Hennig J; Hub JS
J Chem Theory Comput; 2019 Aug; 15(8):4687-4698. PubMed ID: 31251056
[TBL] [Abstract][Full Text] [Related]
15. Coarse-Grained Molecular Modeling of the Solution Structure Ensemble of Dengue Virus Nonstructural Protein 5 with Small-Angle X-ray Scattering Intensity.
Zhu G; Saw WG; Nalaparaju A; Grüber G; Lu L
J Phys Chem B; 2017 Mar; 121(10):2252-2264. PubMed ID: 28224788
[TBL] [Abstract][Full Text] [Related]
16. Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics.
Shevchuk R; Hub JS
PLoS Comput Biol; 2017 Oct; 13(10):e1005800. PubMed ID: 29045407
[TBL] [Abstract][Full Text] [Related]
17. Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data.
Pesce F; Lindorff-Larsen K
Biophys J; 2021 Nov; 120(22):5124-5135. PubMed ID: 34627764
[TBL] [Abstract][Full Text] [Related]
18. Methods for SAXS-based structure determination of biomolecular complexes.
Yang S
Adv Mater; 2014 Dec; 26(46):7902-10. PubMed ID: 24888261
[TBL] [Abstract][Full Text] [Related]
19. SAXS-Oriented Ensemble Refinement of Flexible Biomolecules.
Cheng P; Peng J; Zhang Z
Biophys J; 2017 Apr; 112(7):1295-1301. PubMed ID: 28402873
[TBL] [Abstract][Full Text] [Related]
20. SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes.
Zhao C; Shukla D
Sci Rep; 2018 Dec; 8(1):17748. PubMed ID: 30531946
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]