Cited by 245Protein Structure and DynamicsRNA and protein synthesis mechanismsChemical Synthesis and Analysis

Specific interactions for ab initio folding of protein terminal regions with secondary structures

Yang, Yuedong, Zhou, Yaoqi·2008·Proteins Structure Function and Bioinformatics

Abstract

Proteins fold into unique three-dimensional structures by specific, orientation-dependent interactions between amino acid residues. Here, we extract orientation-dependent interactions from protein structures by treating each polar atom as a dipole with a direction. The resulting statistical energy function successfully refolds 13 out of 16 fully unfolded secondary-structure terminal regions of 10-23 amino acid residues in 15 small proteins. Dissecting the orientation-dependent energy function reveals that the orientation preference between hydrogen-bonded atoms is not enough to account for the structural specificity of proteins. The result has significant implications on the theoretical and experimental searches for specific interactions involved in protein folding and molecular recognition between proteins and other biologically active molecules.

Integrity signals

Registry

Crossref · 10.1002/prot.21968

Cites

42 of 42 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?

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Yang, Y., & Zhou, Y.
Affiliations
  • Indiana University Indianapolis (US)
  • Indiana University School of Medicine (US)
Corresponding author
Zhou, Yaoqi
Venue
Proteins Structure Function and Bioinformatics
Publisher
Wiley
Published
2008-02-07
Volume
72
Issue
2
Pages
793-803
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
OpenAlex
W2008505479
Cited by
245
References
42
Citations by year
2026: 2 · 2025: 7 · 2024: 2 · 2023: 4 · 2022: 6 · 2021: 15 · 2020: 23 · 2019: 24 · 2018: 19 · 2017: 21 · 2016: 20 · 2015: 15 · 2014: 28 · 2013: 23 · 2012: 15
FWCI
2.88
Type
journal article
Language
en
Open access
closed
Locations
  • Proteins Structure Function and Bioinformatics (publishedVersion)
  • PubMed (publishedVersion)
  • Griffith Research Online (submittedVersion)
Funders
National Institute of General Medical Sciences (R0I GM 966049, R0I GM 068530)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
Keywords
protein folding, orientation-dependent interactions, secondary structure, hydrogen bonding, molecular recognition
MeSH terms
Algorithms, Hydrogen Bonding, Proteins, Protein Structure, Secondary, Protein Folding, Databases, Protein

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