[HTML][HTML] Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

D Liebschner, PV Afonine, ML Baker… - Biological …, 2019 - journals.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods
to determine three-dimensional macromolecular structures, which are required to …

Small-angle X-ray and neutron scattering

CM Jeffries, J Ilavsky, A Martel, S Hinrichs… - Nature Reviews …, 2021 - nature.com
Small-angle scattering (SAS) is a technique that is able to probe the structural organization
of matter and quantify its response to changes in external conditions. X-ray and neutron …

US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes

C Zhang, M Shine, AM Pyle, Y Zhang - Nature methods, 2022 - nature.com
Abstract Structure comparison and alignment are of fundamental importance in structural
biology studies. We developed the first universal platform, US-align, to uniformly align …

[HTML][HTML] ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

K Manalastas-Cantos, PV Konarev… - Applied …, 2021 - journals.iucr.org
The ATSAS software suite encompasses a number of programs for the processing,
visualization, analysis and modelling of small-angle scattering data, with a focus on the data …

RCSB Protein Data Bank: architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive

Y Rose, JM Duarte, R Lowe, J Segura, C Bi… - Journal of molecular …, 2021 - Elsevier
Abstract The US Research Collaboratory for Structural Bioinformatics Protein Data Bank
(RCSB PDB) serves many millions of unique users worldwide by delivering experimentally …

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python

S Zhang, JM Krieger, Y Zhang, C Kaya, B Kaynak… - …, 2021 - academic.oup.com
ProDy, an integrated application programming interface developed for modelling and
analysing protein dynamics, has significantly evolved in recent years in response to the …

Principles of the battery data genome

L Ward, S Babinec, EJ Dufek, DA Howey… - Joule, 2022 - cell.com
Batteries are central to modern society. They are no longer just a convenience but a critical
enabler of the transition to a resilient, low-carbon economy. Battery development capabilities …

The protein data bank archive

S Velankar, SK Burley, G Kurisu, JC Hoch… - Structural Proteomics …, 2021 - Springer
Abstract Protein Data Bank is the single worldwide archive of experimentally determined
macromolecular structure data. Established in 1971 as the first open access data resource in …

PDBx/mmCIF ecosystem: foundational semantic tools for structural biology

JD Westbrook, JY Young, C Shao, Z Feng… - Journal of molecular …, 2022 - Elsevier
Abstract PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular
Crystallographic Information Framework (mmCIF), has become the data standard for …

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

C Tan, J Jung, C Kobayashi, DUL Torre… - PLOS Computational …, 2022 - journals.plos.org
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …