Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.
Journal, issue, pages	J Struct Biol, Vol. 160, Issue 1, Page 11-27, Year 2007
Publish date	Jul 6, 2007
Authors	Xiangan Liu / Wen Jiang / Joanita Jakana / Wah Chiu /
PubMed Abstract	Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of ...Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of optimization algorithm, for globally aligning the center and orientation of a particle simultaneously. A consistency criterion was developed to ensure the alignment parameters are correct and to remove some bad particles from a large pool of images of icosahedral particles. Without using any a priori model, this procedure is able to reconstruct a structure from a random initial model. Combining the procedure above with a new empirical double threshold particle selection method, we are able to pick tens of best quality particles to reconstruct a subnanometer resolution map from scratch. Using the best 62 particles of rice dwarf virus, the reconstruction reached 9.6A resolution at which four helices of the P3A subunit of RDV are resolved. Furthermore, with the 284 best particles, the reconstruction is improved to 7.9A resolution, and 21 of 22 helices and six of seven beta sheets are resolved.
External links	J Struct Biol / PubMed:17698370 / PubMed Central
Methods	EM (single particle)
Resolution	7.9 - 9.8 Å
Structure data	EMDB-1375: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 7.9 Å EMDB-1376: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 7.9 Å EMDB-1377: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.3 Å EMDB-1378: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.3 Å EMDB-1379: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.3 Å EMDB-1380: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.3 Å EMDB-1381: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.6 Å EMDB-1382: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.6 Å EMDB-1383: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.9 Å EMDB-1384: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 8.9 Å EMDB-1385: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.2 Å EMDB-1386: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.2 Å EMDB-1387: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.6 Å EMDB-1388: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.6 Å EMDB-1389: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.8 Å EMDB-1390: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. Method: EM (single particle) / Resolution: 9.8 Å