ArticleActa crystallographica. Section D, Biological crystallography2008
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis.
Article in Acta crystallographica. Section D, Biological crystallography, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- ProFlex as a linguistic bridge for decoding protein dynamics in normal mode analysis.Nature communications · 2025Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.Molecular biology and evolution · 2019Article
- Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.Annual review of biophysics · 2016Review
- xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.Acta crystallographica. Section D, Biological crystallography · 2012Article
- Improving the accuracy of macromolecular structure refinement at 7 Å resolution.Structure (London, England : 1993) · 2012Article
- phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.Journal of structural and functional genomics · 2012Article
- AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.Nucleic acids research · 2011Article
- Relationships between structural dynamics and functional kinetics in oligomeric membrane receptors.Biophysical journal · 2010Review
- Interpretation of very low resolution X-ray electron-density maps using core objects.Acta crystallographica. Section D, Biological crystallography · 2009Article
- An introduction to molecular replacement.Acta crystallographica. Section D, Biological crystallography · 2008Article
- BALBES: a molecular-replacement pipeline.Acta crystallographica. Section D, Biological crystallography · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X-ray or cryo-EM), generalizing rigid-body refinement methods by adding just a few additional degrees of freedom that sample collective and large-amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.
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.