ReviewIUCrJ2015
Macromolecular ab initio phasing enforcing secondary and tertiary structure.
Review in IUCrJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 2024Article
- AlphaFold two years on: Validation and impact.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The molecular architecture ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Modes and model building in SHELXE.Acta crystallographica. Section D, Structural biology · 2024Article
- Molecular replacement for small-molecule crystal structure determination from X-ray and electron diffraction data with reduced resolution.Acta crystallographica. Section A, Foundations and advances · 2023Article
- Article
- Molecular Mechanism of STIL Coiled-Coil Domain Oligomerization.International journal of molecular sciences · 2023Article
- Predicted models and CCP4.Acta crystallographica. Section D, Structural biology · 2023Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Fragment-BasedACS bio & med chem Au · 2023Article
- The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline.International journal of molecular sciences · 2023Article
- Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE.Acta crystallographica. Section D, Structural biology · 2022Article
- Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER.Acta crystallographica. Section D, Structural biology · 2022Article
- CCP4 Cloud for structure determination and project management in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2022Article
- Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem.Scientific reports · 2021Article
- Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.Acta crystallographica. Section D, Structural biology · 2020Article
- ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.Acta crystallographica. Section D, Structural biology · 2020Article
- ALIXE: a phase-combination tool for fragment-based molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.Acta crystallographica. Section D, Structural biology · 2020Article
- A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study.Acta crystallographica. Section D, Structural biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.