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

D Liebschner, PV Afonine, ML Baker… - … Section D: Structural …, 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 …

[PDF][PDF] Implications of AlphaFold2 for crystallographic phasing by molecular replacement

AJ McCoy, MD Sammito, RJ Read - Acta Crystallographica Section …, 2022 - journals.iucr.org
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction
(CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein …

Large language models generate functional protein sequences across diverse families

A Madani, B Krause, ER Greene, S Subramanian… - Nature …, 2023 - nature.com
Deep-learning language models have shown promise in various biotechnological
applications, including protein design and engineering. Here we describe ProGen, a …

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 …

Accurate prediction of protein structures and interactions using a three-track neural network

M Baek, F DiMaio, I Anishchenko, J Dauparas… - Science, 2021 - science.org
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …

[PDF][PDF] ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

TI Croll - Acta Crystallographica Section D: Structural Biology, 2018 - journals.iucr.org
This paper introduces ISOLDE, a new software package designed to provide an intuitive
environment for high-fidelity interactive remodelling/refinement of macromolecular models …

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer

JA Mattocks, JJ Jung, CY Lin, Z Dong, NH Yennawar… - Nature, 2023 - nature.com
Technologically critical rare-earth elements are notoriously difficult to separate, owing to
their subtle differences in ionic radius and coordination number,–. The natural lanthanide …

De novo design of potent and selective mimics of IL-2 and IL-15

DA Silva, S Yu, UY Ulge, JB Spangler, KM Jude… - Nature, 2019 - nature.com
We describe a de novo computational approach for designing proteins that recapitulate the
binding sites of natural cytokines, but are otherwise unrelated in topology or amino acid …

[PDF][PDF] Polder maps: improving OMIT maps by excluding bulk solvent

D Liebschner, PV Afonine, NW Moriarty… - … Section D: Structural …, 2017 - journals.iucr.org
The crystallographic maps that are routinely used during the structure-solution workflow are
almost always model-biased because model information is used for their calculation. As …

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

S Akichika, S Hirano, Y Shichino, T Suzuki… - Science, 2019 - science.org
INTRODUCTION N 6-methyladenosine (m6A), an abundant modification in eukaryotic
mRNAs and long-noncoding RNAs, has been recognized as a major epitranscriptome mark …