These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
7. Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy. Dodd T; Yan C; Ivanov I J Chem Inf Model; 2020 May; 60(5):2470-2483. PubMed ID: 32202798 [TBL] [Abstract][Full Text] [Related]
8. Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. Sarkar D; Lee H; Vant JW; Turilli M; Vermaas JV; Jha S; Singharoy A J Chem Inf Model; 2023 Sep; 63(18):5834-5846. PubMed ID: 37661856 [TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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]
11. 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]
12. Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials. Vant JW; Lahey SJ; Jana K; Shekhar M; Sarkar D; Munk BH; Kleinekathöfer U; Mittal S; Rowley C; Singharoy A J Chem Inf Model; 2020 May; 60(5):2591-2604. PubMed ID: 32207947 [TBL] [Abstract][Full Text] [Related]
13. 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]
14. 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]
15. 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]
16. Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches. Miyashita O; Tama F Curr Opin Struct Biol; 2023 Oct; 82():102653. PubMed ID: 37451233 [TBL] [Abstract][Full Text] [Related]
17. Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. Wang Y; Shekhar M; Thifault D; Williams CJ; McGreevy R; Richardson J; Singharoy A; Tajkhorshid E J Struct Biol; 2018 Nov; 204(2):319-328. PubMed ID: 30092279 [TBL] [Abstract][Full Text] [Related]
19. Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. Leelananda SP; Lindert S J Chem Inf Model; 2020 May; 60(5):2522-2532. PubMed ID: 31872764 [TBL] [Abstract][Full Text] [Related]
20. 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] [Next] [New Search]