Deep learning for protein structure prediction and design—progress and applications

J Jänes, P Beltrao - Molecular Systems Biology, 2024 - embopress.org
Proteins are the key molecular machines that orchestrate all biological processes of the cell.
Most proteins fold into three-dimensional shapes that are critical for their function. Studying …

Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy

MC DiIorio, AW Kulczyk - Micromachines, 2023 - mdpi.com
Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method
for near-atomic structure determination, shedding light on the important molecular …

Hybrid computational methods combining experimental information with molecular dynamics

A Mondal, S Lenz, JL MacCallum, A Perez - Current Opinion in Structural …, 2023 - Elsevier
A goal of structural biology is to understand how macromolecules carry out their biological
roles by identifying their metastable states, mechanisms of action, pathways leading to …

[HTML][HTML] An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes

CL McCafferty, O Papoulas, C Lee, KH Bui, DW Taylor… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies
motile ciliopathies, a broad class of human diseases. Motile cilia contain myriad different …

Bayesian methods in integrative structure modeling

M Habeck - Biological Chemistry, 2023 - degruyter.com
There is a growing interest in characterizing the structure and dynamics of large
biomolecular assemblies and their interactions within the cellular environment. A diverse …

An amino acid-resolution interactome for motile cilia identifies the structure and function of ciliopathy protein complexes

CL McCafferty, O Papoulas, C Lee, KH Bui… - Developmental Cell, 2024 - cell.com
Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies
motile ciliopathies, a broad class of human diseases. Motile cilia contain a myriad of different …

Do Not Waste Time─ Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin

L Nouchikian, D Fernandez-Martinez… - Analytical …, 2024 - ACS Publications
Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein
complexes and interactions in living systems. It enables the investigation of many large and …

Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy Topographic Images

JL Pellequer - Journal of Molecular Recognition, 2024 - Wiley Online Library
After the recent double revolutions in structural biology, which include the use of direct
detectors for cryo‐electron microscopy resulting in a significant improvement in the expected …

The dry lab microscopist or prompt microscopist: do we need them?

F Braet, W Cai - Biophysical Reviews, 2024 - Springer
In modern biological microscopy, the explosion of data volume and complexity highlights the
urgent need for specialised data management support roles. While traditional microscopy …

In-cell Structural Biology Through the Integration of Solution NMR Spectroscopy and Computational Science

Y Ito, T Ikeya, K Inomata - 2023 - books.rsc.org
The intracellular environment is highly crowded (molecular crowding) and differs
significantly from the environment in dilute solutions that we usually use in biochemical …