Cross-linking mass spectrometry for investigating protein conformations and protein–protein Interactions─ A method for all seasons

L Piersimoni, PL Kastritis, C Arlt, A Sinz - Chemical Reviews, 2021‏ - ACS Publications
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022‏ - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

UCSF ChimeraX: Tools for structure building and analysis

EC Meng, TD Goddard, EF Pettersen… - Protein …, 2023‏ - Wiley Online Library
Advances in computational tools for atomic model building are leading to accurate models of
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …

The CCP4 suite: integrative software for macromolecular crystallography

J Agirre, M Atanasova, H Bagdonas… - Biological …, 2023‏ - journals.iucr.org
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective
with a mission to develop, test, distribute and promote software for macromolecular …

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

T Tamura, J Ito, K Uriu, J Zahradnik, I Kida… - Nature …, 2023‏ - nature.com
Abstract In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified,
and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that …

[HTML][HTML] Antibody escape of SARS-CoV-2 Omicron BA. 4 and BA. 5 from vaccine and BA. 1 serum

A Tuekprakhon, R Nutalai, A Dijokaite-Guraliuc… - Cell, 2022‏ - cell.com
The Omicron lineage of SARS-CoV-2, which was first described in November 2021, spread
rapidly to become globally dominant and has split into a number of sublineages. BA. 1 …

BA. 2.12. 1, BA. 4 and BA. 5 escape antibodies elicited by Omicron infection

Y Cao, A Yisimayi, F Jian, W Song, T **ao, L Wang… - Nature, 2022‏ - nature.com
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.
2.12. 1, BA. 4 and BA. 5 exhibit higher transmissibility than the BA. 2 lineage. The receptor …

Machine learning-aided engineering of hydrolases for PET depolymerization

H Lu, DJ Diaz, NJ Czarnecki, C Zhu, W Kim, R Shroff… - Nature, 2022‏ - nature.com
Plastic waste poses an ecological challenge,–and enzymatic degradation offers one,
potentially green and scalable, route for polyesters waste recycling. Poly (ethylene …

Automated model building and protein identification in cryo-EM maps

K Jamali, L Käll, R Zhang, A Brown, D Kimanius… - Nature, 2024‏ - nature.com
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high
levels of expertise and labour-intensive manual intervention in three-dimensional computer …

Design of protein-binding proteins from the target structure alone

L Cao, B Coventry, I Goreshnik, B Huang, W Sheffler… - Nature, 2022‏ - nature.com
The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains a challenge …