ArticleActa crystallographica. Section D, Structural biology2023
LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments.
Article in Acta crystallographica. Section D, Structural biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 11 citations in OpenAlex.
- A protein-foldamer supramolecular synthon for self-assembled hybrid architectures.Nature chemistry · 2026Article
- Generation and modulation of catalytically relevant states of a dye-decolourizing peroxidase using time-resolved serial femtosecond crystallography with drop-on-chip mixing and X-ray-driven reduction.Acta crystallographica. Section D, Structural biology · 2026Article
- Exploring the Interactive Effect of Pectins fromACS omega · 2026Article
- Crystallise, poise, capture: a multimodal platform for correlated structural and spectroscopic characterisation of redox enzymes.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2026Article
- Enhancing the Outcome of Crystallographic Fragment Screening by Choosing the Optimal Protein Crystal Form.Small science · 2026Article
- Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?Nature communications · 2026Article
- ProteinsPlus: a publicly available resource for protein structure mining.Nucleic acids research · 2025Article
- Probing Macromolecular Interactions by Loss of Solvent Content in Protein Crystals: Application to the Amyloid‑β Peptide Binding to Transthyretin.Crystal growth & design · 2025Article
- A snapshot love story: what serial crystallography has done and will do for us.Acta crystallographica. Section D, Structural biology · 2024Review
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Authors and funding
7 authors at 2 institutions in 1 country.
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Abstract
Due to the structural complexity of proteins, their corresponding crystal arrangements generally contain a significant amount of solvent-occupied space. These areas allow a certain degree of intracrystalline protein flexibility and mobility of solutes. Therefore, knowledge of the geometry of solvent-filled channels and cavities is essential whenever the dynamics inside a crystal are of interest. Especially in soaking experiments for structure-based drug design, ligands must be able to traverse the crystal solvent channels and reach the corresponding binding pockets. Unsuccessful screenings are sometimes attributed to the geometry of the crystal packing, but the underlying causes are often difficult to understand. This work presents LifeSoaks, a novel tool for analyzing and visualizing solvent channels in protein crystals. LifeSoaks uses a Voronoi diagram-based periodic channel representation which can be efficiently computed. The size and location of channel bottlenecks, which might hinder molecular diffusion, can be directly derived from this representation. This work presents the calculated bottleneck radii for all crystal structures in the PDB and the analysis of a new, hand-curated data set of structures obtained by soaking experiments. The results indicate that the consideration of bottleneck radii and the visual inspection of channels are beneficial for planning soaking experiments.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.