Cited by 206Protein Structure and DynamicsEnzyme Structure and FunctionAdvanced Electron Microscopy Techniques and Applications

Integrating diverse data for structure determination of macromolecular assemblies

Alber, Frank, Förster, Friedrich, Korkin, Dmitry, Topf, Maya, Sali, Andrej·2008·Annual Review of Biochemistry

Abstract

To understand the cell, we need to determine the macromolecular assembly structures, which may consist of tens to hundreds of components. First, we review the varied experimental data that characterize the assemblies at several levels of resolution. We then describe computational methods for generating the structures using these data. To maximize completeness, resolution, accuracy, precision, and efficiency of the structure determination, a computational approach is required that uses spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. This approach is illustrated by determining the configuration of the 456 proteins in the nuclear pore complex (NPC) from baker's yeast. With these tools, we are poised to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework.

Integrity signals

Registry

Crossref · 10.1146/annurev.biochem.77.060407.135530

Cites

187 of 187 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Complementary measurement techniques are beneficial and may ultimately be necessary to gain a full understanding of biological structure across multiple scales.

    “A core concept is that complementary measurement techniques are not only beneficial in general, but they may ultimately be necessary to gain a full understanding of biological structure across multiple scales.”

    From Mapping the multiscale structure of biological systems (2021) · cites this paper as Alber et al., 2008

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Alber, F., Förster, F., Korkin, D., Topf, M., & Sali, A.
Affiliations
  • QB3 (US)
  • Birkbeck, University of London (GB)
  • Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California at San Francisco, California 94158-2330;
Venue
Annual Review of Biochemistry
Published
2008-06-01
Volume
77
Issue
1
Pages
443-477
ISSN
  • 0066-4154 (ISSN-L)
  • 1545-4509
OpenAlex
W2887067015
Cited by
206
References
187
Citations by year
2025: 1 · 2023: 2 · 2022: 5 · 2021: 9 · 2020: 7 · 2019: 14 · 2018: 7 · 2017: 16 · 2016: 11 · 2015: 17 · 2014: 17 · 2013: 19 · 2012: 25
FWCI
1.44
Type
journal article
Language
en
Open access
closed
Locations
  • Annual Review of Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
  • BIROn (Birkbeck, University of London) (submittedVersion)
Funders
  • National Institute of General Medical Sciences (R01GM054762, R01 GM54762)
  • National Center for Research Resources (U54RR022220)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Keywords
nuclear pore complex, scoring functions, structural optimization, protein complexes, Saccharomyces cerevisiae
MeSH terms
Animals, Biochemistry, Biophysics, Humans, Microscopy, Electron, Models, Molecular, Molecular Conformation, Magnetic Resonance Spectroscopy, Saccharomyces cerevisiae, Scattering, Radiation, Mass Spectrometry, X-Rays, Reproducibility of Results, Nuclear Pore, Macromolecular Substances

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review