logo3

Newsletter No. 488
April 17, 2023

ACA News, IUCr Newsletter, IUCr Meetings List


MARCH 2023 PUBLICATIONS BY MEMBERS OF THE GROUP

1: Dearborn AD, Kumar A, Marcotrigiano J. Learning more about hepatitis E virus.
Elife. 2023 Mar 22;12:e87047. doi: 10.7554/eLife.87047. PMID: 36947136; PMCID:
PMC10032651.

2: Zhan J, Xia D. Bcs1, a novel target for fungicide. Front Chem. 2023 Mar
13;11:1146753. doi: 10.3389/fchem.2023.1146753. PMID: 36993815; PMCID:
PMC10040684.

3: Park JE, Lee H, Oliva P, Kirsch K, Kim B, Ahn JI, Alverez CN, Gaikwad S,
Krausz KW, O'Connor R, Rai G, Simeonov A, Mock BA, Gonzalez FJ, Lee KS, Jacobson
KA. Structural Optimization and Anticancer Activity of Polo-like Kinase 1 (Plk1)
Polo-Box Domain (PBD) Inhibitors and Their Prodrugs
. ACS Pharmacol Transl Sci.
2023 Feb 20;6(3):422-446. doi: 10.1021/acsptsci.2c00250. PMID: 36926457; PMCID:
PMC10012257.

4: Stamos JD, Rahman MA, Gorini G, Silva de Castro I, Becerra-Flores M, Van
Wazer DJ, N'Guessan KF, Clark NM, Bissa M, Gutowska A, Mason RD, Kim J, Rao M,
Roederer M, Paquin-Proulx D, Evans DT, Cicala C, Arthos J,
Kwong PD, Zhou T,
Cardozo T, Franchini G. Effect of Passive Administration of Monoclonal
Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like
Coil/Helical or β-Sheet Conformations on Time of SIV<sub>mac251</sub>
Acquisition
. J Virol. 2023 Mar 28:e0186422. doi: 10.1128/jvi.01864-22. Epub
ahead of print. PMID: 36976017.

5: Tripathi P, Bender MF, Lei H, Da Silva Pereira L, Shen CH, Bonilla B, Dillon
M, Ou L, Pancera M, Wang LT, Zhang B, Batista FD, Idris AH, Seder RA,
Kwong PD.
Cryo-EM structures of anti-malarial antibody L9 with circumsporozoite protein
reveal trimeric L9 association and complete 27-residue epitope
. Structure. 2023
Mar 15:S0969-2126(23)00043-6. doi: 10.1016/j.str.2023.02.009. Epub ahead of
print. PMID: 36931276.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS CryoEM: Grid Screening & Data Acquisition

 A. Cheng et al., "Fully automated multi-grid cryoEM screening using Smart Leginon"

 P.T. Kim et al., "Learning to automate cryo-electron microscopy data collection with Ptolemy"

ARCHIVE: Introduction, Sample Preparation, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Other Biophysical Methods, Integrative Structure Determination.

DISCUSSIONS - Suggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation, Table 1,   Protein Data Bank & Protein Folding.

READINGS AND TUTORIALS - Evolutionay-scale structure prediction

Z. Lin et al., "Evolutionary-scale prediction of atomic-level protein structure with a language model" (2023)

D.N. Woolfson, "Understanding a protein fold: the physics, chemistry, and biology of alpha-helical coiled coils" (2023)

G. Huang, C. Zeng, Y. Shi, "Structure of the nuclear pore complex goes atomic" (2023)

T. Blundell, "Structural Biology, Bioinformatics and Drug Discovery: Six Decades of Science & Its Applications" (2022)


ARCHIVE: Crystallography, Data AquisitionStructural BiologyStructure Prediction


 LINKS Suggestions?

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources, AlphaFold DB,
                  virusMED, BioCyc, RaMP-DB,


Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib, Robetta (RoseTTAFold),

Copyright © NIH X-Ray Diffraction Interest Group                       Maintained by Dr. Xinhua Ji