Cited by 863Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

Correlated mutations and residue contacts in proteins

Open access
Göbel, Ulrike, Sander, Chris, Schneider, Reinhard, Valencia, Alfonso·1994·Proteins Structure Function and Bioinformatics

Abstract

The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information.

Integrity signals

Registry

Crossref · 10.1002/prot.340180402

Cites

17 of 17 references verified0 citation errors · 0 not checkable

Statistics

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

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Göbel, U., Sander, C., Schneider, R., & Valencia, A.
Affiliations
European Molecular Biology Laboratory (DE)
Corresponding author
Sander, Chris
Venue
Proteins Structure Function and Bioinformatics
Publisher
Wiley
Published
1994-04
Volume
18
Issue
4
Pages
309-317
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
OpenAlex
W2171641243
Cited by
863
References
17
Citations by year
2026: 11 · 2025: 18 · 2024: 22 · 2023: 36 · 2022: 22 · 2021: 42 · 2020: 32 · 2019: 42 · 2018: 36 · 2017: 36 · 2016: 39 · 2015: 30 · 2014: 37 · 2013: 34 · 2012: 48
FWCI
4.54
Type
journal article
Language
en
Open access
Locations
  • Proteins Structure Function and Bioinformatics (publishedVersion)
  • PubMed (publishedVersion)
  • Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
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 › Molecular Biology › Machine Learning in Bioinformatics
Keywords
correlated mutations, residue contacts, contact map prediction, protein evolution, multiple sequence alignment, protein tertiary structure, protein families, protein structure prediction from sequence
MeSH terms
Amino Acid Sequence, Biological Evolution, Mathematical Computing, Models, Genetic, Models, Molecular, Models, Theoretical, Molecular Sequence Data, Mutation, Proteins, Ribonuclease, Pancreatic, Structure-Activity Relationship, Trypsin Inhibitors, Sequence Alignment, Protein Structure, Secondary, Crystallography, X-Ray

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