CoChat
Sign Up
Cited by 1,833Protein Structure and DynamicsEnzyme Structure and FunctionGenomics and Phylogenetic Studies

Twilight zone of protein sequence alignments

Rost, Burkhard·1999·Protein Engineering, Design and Selection
DOI 10.1093/protein/12.2.85
Open this paper in CoChat — free account

Abstract

Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments). The signal gets blurred in the twilight zone of 20-35% sequence identity. Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. Four results stood out. (i) The transition from the safe zone of sequence alignment into the twilight zone is described by an explosion of false negatives. More than 95% of all pairs detected in the twilight zone had different structures. More precisely, above a cut-off roughly corresponding to 30% sequence identity, 90% of the pairs were homologous; below 25% less than 10% were. (ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. For example, if 10 residues were similar in an alignment of length 16 (>60%), structural similarity could not be inferred. (iii) The 'more similar than identical' rule (discarding all pairs for which percentage similarity was lower than percentage identity) reduced false positives significantly. (iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. All findings are applicable to automatic database searches.

Integrity signals

Registry

Crossref · 10.1093/protein/12.2.85

Cites

61 of 61 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?

  • The model learned evolutionary conservation patterns without being trained on explicit alignment information.

    “This indicates that the model has captured evolutionary conservation patterns without training on explicit alignment information such as with Potts models51, as implemented in direct coupling analysis7,52–55.”

    From Large language models generate functional protein sequences across diverse families (2023) · cites this paper as [53]

  • Above 30% sequence identity, structure and function are usually conserved between natural proteins.

    “Above 30% sequence identity, structure and function are usually conserved between natural proteins 59.”

    From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [59]

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Related

Authors
Rost, B.
Affiliations
European Molecular Biology Laboratory (DE)
Corresponding author
Rost, Burkhard
ORCID
Rost, Burkhard
Venue
Protein Engineering, Design and Selection
Publisher
Oxford University Press (OUP)
Published
1999-02
Volume
12
Issue
2
Pages
85-94
ISSN
  • 0269-2139 (ISSN-L)
  • 1741-0134
  • 1741-0126
DOI
10.1093/protein/12.2.85
OpenAlex
W2101220662
Cited by
1,833
References
61
Citations by year
2026: 106 · 2025: 84 · 2024: 86 · 2023: 80 · 2022: 90 · 2021: 95 · 2020: 78 · 2019: 82 · 2018: 67 · 2017: 65 · 2016: 100 · 2015: 63 · 2014: 68 · 2013: 78 · 2012: 60
FWCI
8.84
Type
journal article
Language
en
Open access
closed
Locations
  • Protein Engineering Design and Selection (publishedVersion)
  • PubMed (publishedVersion)
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 › Genomics and Phylogenetic Studies
Keywords
protein sequence alignment, twilight zone, sequence identity, structural homology, false positives, database searching, homology detection
MeSH terms
Computer Simulation, False Positive Reactions, Models, Statistical, Databases, Factual, Sequence Alignment, Sequence Homology, Amino Acid

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