| Newsletter No. 452
|| October 4, 2021
| METHODS - Evolving data standards for cryo-EM structures
The development of cryo-EM is directly reflected by the growth of cryo-EM strructure depositions contributed worldwide to public data archived. The archiving systems and underlying data standards supporting depostioin, annotation, release, and validation of cyro-EM stuctures and the associated metadata describing cryo-EM experiments have been developed over time to support this growth. Recently, CL Lawson, HM Berman, and W Chiu outlined the history of these systems and described the process by which data standards had been developed. For details, please click the link.
ARCHIVE: Introduction, Sample Preparation, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Other Biophysical Methods.
|DISCUSSIONS - How Many More Structures Are Needed to Train AI for
Prediction of "Highly Accurate" 3D Structures Based on Any Sequence?
ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in Crystallography, Absorption Correction, Data for Refinement and Publication, Validation, Table 1.
| READINGS AND TUTORIALS - The Future of Structural Biology
Google Research, "Everyone wants to do the model work, not the data work": Data Cascades in High-Stakes AI (2021)
AlphaFold DB, Great expectations - the potential impacts of AlphaFold DB (2021)
AlphaFold, Highly accurate protein structure prediction with AlphaFold (2021)
RoseTTAFold, Accurate prediction of protein structures and interactions using a three-track neural network (2021)
Stephen Burley, The Future of Structural Biology from a Global Perspective (2021)
Joachim Frank, Single-Partical Cryo-EM: Visualizing Biological Molecules in Their Native State (2021)
ARCHIVE: 2005 - 2020.
| LINKS - Robetta (Link), with RoseTTAFold as a new addition
Databases: DisProt, ExPASy, HAD, HIC-Up, NDB, PDB, PDBe, Protein Geometry
SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources, AlphaFold DB,
Programs: CCP4, COOT, DSSR, HKL, PHENIX, PyMOL, SOLVE, XDS
Servers: ACHESYM, Anisotropy, C6@C3, Dali, ESPript, Grade, PDBePISA, Phyre2,
MolProbity, RestraintLib, Robetta,
|Copyright © NIH X-Ray Diffraction Group Maintained by Dr. Xinhua Ji|