Macromolecular room temperature crystallography

M Fischer - Quarterly Reviews of Biophysics, 2021 - cambridge.org
X-ray crystallography enables detailed structural studies of proteins to understand and
modulate their function. Conducting crystallographic experiments at cryogenic temperatures …

[HTML][HTML] Representing structures of the multiple conformational states of proteins

TA Ramelot, R Tejero, GT Montelione - Current Opinion in Structural …, 2023 - Elsevier
Biomolecules exhibit dynamic behavior that single-state models of their structures cannot
fully capture. We review some recent advances for investigating multiple conformations of …

Ligand binding remodels protein side-chain conformational heterogeneity

SA Wankowicz, SH de Oliveira, DW Hogan… - Elife, 2022 - elifesciences.org
While protein conformational heterogeneity plays an important role in many aspects of
biological function, including ligand binding, its impact has been difficult to quantify …

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

SE Hoff, FE Thomasen, K Lindorff-Larsen… - PLOS Computational …, 2024 - journals.plos.org
Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a
challenging problem of outstanding importance. Current refinement methods often generate …

A pocket-based 3D molecule generative model fueled by experimental electron density

L Wang, R Bai, X Shi, W Zhang, Y Cui, X Wang… - Scientific reports, 2022 - nature.com
We report for the first time the use of experimental electron density (ED) as training data for
the generation of drug-like three-dimensional molecules based on the structure of a target …

[PDF][PDF] Best practices for time-resolved serial synchrotron crystallography

EC Schulz, BA Yorke, AR Pearson… - … Section D: Structural …, 2022 - journals.iucr.org
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-
resolved crystallographic experiments, which were originally the preserve of a few expert …

The impact of library size and scale of testing on virtual screening

F Liu, O Mailhot, IS Glenn, SF Vigneron… - Nature Chemical …, 2025 - nature.com
Virtual ligand libraries for ligand discovery have recently increased 10,000-fold. Whether this
has improved hit rates and potencies has not been directly tested. Meanwhile, typically only …

[PDF][PDF] FLEXR: automated multi-conformer model building using electron-density map sampling

TR Stachowski, M Fischer - Acta Crystallographica Section D …, 2023 - journals.iucr.org
Protein conformational dynamics that may inform biology often lie dormant in high-resolution
electron-density maps. While an estimated∼ 18% of side chains in high-resolution models …

Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics

I Boulos, J Jabbour, S Khoury, N Mikhael, V Tishkova… - Molecules, 2023 - mdpi.com
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories:
intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome …

Uncovering protein ensembles: automated multiconformer model building for X-ray crystallography and cryo-EM

SA Wankowicz, A Ravikumar, S Sharma, BT Riley… - …, 2024 - pmc.ncbi.nlm.nih.gov
In their folded state, biomolecules exchange between multiple conformational states that are
crucial for their function. Traditional structural biology methods, such as X-ray …