345 related articles for article (PubMed ID: 21893283)
1. 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]
2. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.
Wu X; Subramaniam S; Case DA; Wu KW; Brooks BR
J Struct Biol; 2013 Sep; 183(3):429-440. PubMed ID: 23876978
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. 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]
5. 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]
6. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.
Dror O; Lasker K; Nussinov R; Wolfson H
Acta Crystallogr D Biol Crystallogr; 2007 Jan; 63(Pt 1):42-9. PubMed ID: 17164525
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.
Bonomi M; Hanot S; Greenberg CH; Sali A; Nilges M; Vendruscolo M; Pellarin R
Structure; 2019 Jan; 27(1):175-188.e6. PubMed ID: 30393052
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.
Jolley CC; Wells SA; Fromme P; Thorpe MF
Biophys J; 2008 Mar; 94(5):1613-21. PubMed ID: 17993504
[TBL] [Abstract][Full Text] [Related]
11. Real-space refinement with DireX: from global fitting to side-chain improvements.
Wang Z; Schröder GF
Biopolymers; 2012 Sep; 97(9):687-97. PubMed ID: 22696405
[TBL] [Abstract][Full Text] [Related]
12. Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.
Singharoy A; Teo I; McGreevy R; Stone JE; Zhao J; Schulten K
Elife; 2016 Jul; 5():. PubMed ID: 27383269
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. Cryo-EM of macromolecular assemblies at near-atomic resolution.
Baker ML; Zhang J; Ludtke SJ; Chiu W
Nat Protoc; 2010 Sep; 5(10):1697-708. PubMed ID: 20885381
[TBL] [Abstract][Full Text] [Related]
15. Docking structures of domains into maps from cryo-electron microscopy using local correlation.
Roseman AM
Acta Crystallogr D Biol Crystallogr; 2000 Oct; 56(Pt 10):1332-40. PubMed ID: 10998630
[TBL] [Abstract][Full Text] [Related]
16. FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.
Saha M; Morais MC
Bioinformatics; 2012 Dec; 28(24):3265-73. PubMed ID: 23131460
[TBL] [Abstract][Full Text] [Related]
17. EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps.
Lasker K; Dror O; Shatsky M; Nussinov R; Wolfson HJ
IEEE/ACM Trans Comput Biol Bioinform; 2007; 4(1):28-39. PubMed ID: 17277411
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Protein-Protein Modeling Using Cryo-EM Restraints.
Trellet M; van Zundert G; Bonvin AMJJ
Methods Mol Biol; 2020; 2112():145-162. PubMed ID: 32006284
[TBL] [Abstract][Full Text] [Related]
20. Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.
Vashisth H; Skiniotis G; Brooks CL
J Phys Chem B; 2013 Apr; 117(14):3738-46. PubMed ID: 23506287
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
