ArticleCommunications biology2022
Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Quantifying optical scattering losses in pump-probe serial femtosecond crystallography experiments.IUCrJ · 2026Article
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- Decarboxylation via a Higher Electronic Excited State Drives LSSmOrange Photoconversion.ACS physical chemistry Au · 2026Article
- Inferring structure factors of weakly populated excited states in perturbative crystallography experiments.bioRxiv : the preprint server for biology · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
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- Sensitive detection of structural dynamics using a statistical framework for comparative crystallography.Science advances · 2025Article
- Denoising and iterative phase recovery reveal low-occupancy populations in protein crystals.Communications biology · 2025Article
- Room-temperature X-ray fragment screening with serial crystallography.Nature communications · 2025Article
- Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states.Nature structural & molecular biology · 2025Article
- Apo-state structure of the metabotropic glutamate receptor 5 transmembrane domain obtained using a photoswitchable ligand.Protein science : a publication of the Protein Society · 2025Article
- TheJournal of applied crystallography · 2025Article
- Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.Science advances · 2025Article
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Abstract
Unstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography.
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