Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Atom depth in protein structure and function.

Alessandro Pintar1, Oliviero Carugo, Sándor Pongor

  • 1Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy. pintar@icgeb.org

Trends in Biochemical Sciences
|November 11, 2003
PubMed
Summary

Atom depth, a measure of protein atom proximity to water, offers insights into protein interiors. This simple geometric descriptor correlates with protein stability, domain size, and residue properties.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.

Bioinformatics advances·2025
Same author

Smart epidemic control: A hybrid model blending ODEs and agent-based simulations for optimal, real-world intervention planning.

PLoS computational biology·2025
Same author

What Is the Crystallographic Resolution of Structural Models of Proteins Generated with AlphaFold2?

ACS chemical biology·2024
Same author

Accuracy of AlphaFold models: Comparison with short N<sup></sup>O contacts in atomic resolution protein crystal structures.

Computational biology and chemistry·2024
Same author

Location of S-nitrosylated cysteines in protein three-dimensional structures.

Proteins·2023
Same author

Automated identification of chalcogen bonds in AlphaFold protein structure database files: is it possible?

Frontiers in molecular biosciences·2023

Area of Science:

  • Structural bioinformatics
  • Computational biophysics

Background:

  • Atom depth is a geometrical descriptor of protein interiors.
  • It complements solvent accessible surface area and buried surface area calculations.
  • Depth is easily computed from protein 3D structures.

Purpose of the Study:

  • To highlight the value of atom depth as a protein descriptor.
  • To showcase its correlations with various protein properties.

Main Methods:

  • Computation of atom depth from protein 3D structures.
  • Statistical analysis of correlations between atom depth and other molecular properties.

Main Results:

  • Atom depth is correlated with protein domain size and stability.

Related Experiment Videos

  • It also correlates with hydrophobicity, residue conservation, and amide proton exchange rates.
  • These findings underscore atom depth's utility in understanding protein characteristics.

    • Conclusions:

    • Atom depth is a valuable and easily computable descriptor for protein interiors.
    • It provides complementary information to surface area calculations.
    • Its correlations reveal insights into protein molecular, residue, and atomic properties.