138 related articles for article (PubMed ID: 37661856)
1. 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]
2. 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]
3. 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]
4. CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.
Qi Y; Lee J; Singharoy A; McGreevy R; Schulten K; Im W
J Phys Chem B; 2017 Apr; 121(15):3718-3723. PubMed ID: 27936734
[TBL] [Abstract][Full Text] [Related]
5. MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.
Dahmani ZL; Scott AL; Vénien-Bryan C; Perahia D; Costa MGS
J Chem Inf Model; 2024 Jun; ():. PubMed ID: 38907694
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. 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]
8. 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]
9. 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]
10. 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]
11. 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]
12. 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]
13. 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]
14. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.
McGreevy R; Teo I; Singharoy A; Schulten K
Methods; 2016 May; 100():50-60. PubMed ID: 26804562
[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. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.
Leelananda SP; Lindert S
J Chem Theory Comput; 2017 Oct; 13(10):5131-5145. PubMed ID: 28949136
[TBL] [Abstract][Full Text] [Related]
17. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.
Zhu J; Cheng L; Fang Q; Zhou ZH; Honig B
J Mol Biol; 2010 Apr; 397(3):835-51. PubMed ID: 20109465
[TBL] [Abstract][Full Text] [Related]
18. Automated simulation-based membrane protein refinement into cryo-EM data.
Yvonnesdotter L; Rovšnik U; Blau C; Lycksell M; Howard RJ; Lindahl E
Biophys J; 2023 Jul; 122(13):2773-2781. PubMed ID: 37277992
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps.
Vashisth H; Skiniotis G; Brooks CL
Structure; 2012 Sep; 20(9):1453-62. PubMed ID: 22958641
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]