258 related articles for article (PubMed ID: 35150654)
1. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements.
Vuillemot R; Miyashita O; Tama F; Rouiller I; Jonic S
J Mol Biol; 2022 Apr; 434(7):167483. PubMed ID: 35150654
[TBL] [Abstract][Full Text] [Related]
2. Cryo_fit: Democratization of flexible fitting for cryo-EM.
Kim DN; Moriarty NW; Kirmizialtin S; Afonine PV; Poon B; Sobolev OV; Adams PD; Sanbonmatsu K
J Struct Biol; 2019 Oct; 208(1):1-6. PubMed ID: 31279069
[TBL] [Abstract][Full Text] [Related]
3. A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit).
Costa MGS; Fagnen C; Vénien-Bryan C; Perahia D
J Chem Inf Model; 2020 May; 60(5):2419-2423. PubMed ID: 31944765
[TBL] [Abstract][Full Text] [Related]
4. Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.
Zheng W
Biophys J; 2011 Jan; 100(2):478-88. PubMed ID: 21244844
[TBL] [Abstract][Full Text] [Related]
5. Applications of the molecular dynamics flexible fitting method.
Trabuco LG; Schreiner E; Gumbart J; Hsin J; Villa E; Schulten K
J Struct Biol; 2011 Mar; 173(3):420-7. PubMed ID: 20932910
[TBL] [Abstract][Full Text] [Related]
6. MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation.
Vuillemot R; Mirzaei A; Harastani M; Hamitouche I; Fréchin L; Klaholz BP; Miyashita O; Tama F; Rouiller I; Jonic S
J Mol Biol; 2023 May; 435(9):167951. PubMed ID: 36638910
[TBL] [Abstract][Full Text] [Related]
7. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.
Trabuco LG; Villa E; Schreiner E; Harrison CB; Schulten K
Methods; 2009 Oct; 49(2):174-80. PubMed ID: 19398010
[TBL] [Abstract][Full Text] [Related]
8. Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.
Dou H; Burrows DW; Baker ML; Ju T
Biophys J; 2017 Jun; 112(12):2479-2493. PubMed ID: 28636906
[TBL] [Abstract][Full Text] [Related]
9. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method.
Chan KY; Trabuco LG; Schreiner E; Schulten K
Biopolymers; 2012 Sep; 97(9):678-86. PubMed ID: 22696404
[TBL] [Abstract][Full Text] [Related]
10. Symmetry-restrained flexible fitting for symmetric EM maps.
Chan KY; Gumbart J; McGreevy R; Watermeyer JM; Sewell BT; Schulten K
Structure; 2011 Sep; 19(9):1211-8. PubMed ID: 21893283
[TBL] [Abstract][Full Text] [Related]
11. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Trabuco LG; Villa E; Mitra K; Frank J; Schulten K
Structure; 2008 May; 16(5):673-83. PubMed ID: 18462672
[TBL] [Abstract][Full Text] [Related]
12. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
Mori T; Kulik M; Miyashita O; Jung J; Tama F; Sugita Y
Structure; 2019 Jan; 27(1):161-174.e3. PubMed ID: 30344106
[TBL] [Abstract][Full Text] [Related]
13. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.
Ahmed A; Whitford PC; Sanbonmatsu KY; Tama F
J Struct Biol; 2012 Feb; 177(2):561-70. PubMed ID: 22019767
[TBL] [Abstract][Full Text] [Related]
14. Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.
Yamamori Y; Tomii K
Int J Mol Sci; 2022 Feb; 23(4):. PubMed ID: 35216093
[TBL] [Abstract][Full Text] [Related]
15. CryoFold 2.0: Cryo-EM Structure Determination with MELD.
Chang L; Mondal A; MacCallum JL; Perez A
J Phys Chem A; 2023 May; 127(17):3906-3913. PubMed ID: 37084537
[TBL] [Abstract][Full Text] [Related]
16. Computational methods for constructing protein structure models from 3D electron microscopy maps.
Esquivel-Rodríguez J; Kihara D
J Struct Biol; 2013 Oct; 184(1):93-102. PubMed ID: 23796504
[TBL] [Abstract][Full Text] [Related]
17. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.
Ahmed A; Tama F
J Struct Biol; 2013 May; 182(2):67-77. PubMed ID: 23416197
[TBL] [Abstract][Full Text] [Related]
18. High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data.
Zheng W; Tekpinar M
Adv Protein Chem Struct Biol; 2014; 96():267-84. PubMed ID: 25443961
[TBL] [Abstract][Full Text] [Related]
19. A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps.
Zhang B; Zhang X; Pearce R; Shen HB; Zhang Y
J Mol Biol; 2020 Sep; 432(19):5365-5377. PubMed ID: 32771523
[TBL] [Abstract][Full Text] [Related]
20. Application of conformational space annealing to the protein structure modeling using cryo-EM maps.
Park J; Joung I; Joo K; Lee J
J Comput Chem; 2023 Nov; 44(30):2332-2346. PubMed ID: 37585026
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
