Towards realizing nano-enabled precision delivery in plants

GV Lowry, JP Giraldo, NF Steinmetz, A Avellan… - Nature …, 2024 - nature.com
Nanocarriers (NCs) that can precisely deliver active agents, nutrients and genetic materials
into plants will make crop agriculture more resilient to climate change and sustainable. As a …

The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

V Agarwal, AC McShan - Nature Chemical Biology, 2024 - nature.com
Artificial intelligence-driven advances in protein structure prediction in recent years have
raised the question: has the protein structure-prediction problem been solved? Here, with a …

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 …

Clustering predicted structures at the scale of the known protein universe

I Barrio-Hernandez, J Yeo, J Jänes, M Mirdita… - Nature, 2023 - nature.com
Proteins are key to all cellular processes and their structure is important in understanding
their function and evolution. Sequence-based predictions of protein structures have …

AlphaFold predictions of fold-switched conformations are driven by structure memorization

D Chakravarty, JW Schafer, EA Chen, JF Thole… - Nature …, 2024 - nature.com
Recent work suggests that AlphaFold (AF)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction

G Terashi, X Wang, D Prasad, T Nakamura, D Kihara - Nature Methods, 2024 - nature.com
Three-dimensional structure modeling from maps is an indispensable step for studying
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …

The ethics of using artificial intelligence in scientific research: new guidance needed for a new tool

DB Resnik, M Hosseini - AI and Ethics, 2024 - Springer
Using artificial intelligence (AI) in research offers many important benefits for science and
society but also creates novel and complex ethical issues. While these ethical issues do not …

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

MF Lensink, G Brysbaert, N Raouraoua… - Proteins: Structure …, 2023 - Wiley Online Library
We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly
prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo …

Critical assessment of methods for predicting the 3D structure of proteins and protein complexes

SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …

AlphaFold2 can predict single-mutation effects

JM McBride, K Polev, A Abdirasulov, V Reinharz… - Physical Review Letters, 2023 - APS
AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation
effects? Here, we report that the localized structural deformation between protein pairs …