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

Three-dimensional computation of atom depth in complex molecular structures.

Daniele Varrazzo1, Andrea Bernini, Ottavia Spiga

  • 1Biomolecular Structure Research Center and Department of Molecular Biology, Università di Siena, I-53100 Siena, Italy.

Bioinformatics (Oxford, England)
|April 14, 2005
PubMed
Summary

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

Amidine isosteric modification tunes proteolytic stability and activity.

RSC chemical biology·2026
Same author

<sup>1</sup>H, <sup>15</sup>N, <sup>13</sup>C backbone resonance assignment of Escherichia coli AlkB in complex with Zn(II) and α-ketoglutarate.

Biomolecular NMR assignments·2026
Same author

Quantifying the Functional Gap in Alkaptonuria Through Machine Learning and Clinical Data Integration.

Bioengineering (Basel, Switzerland)·2026
Same author

A Versatile Strategy for Head-to-Tail Macrocyclization and Traceless Backbone Editing of Short Peptides.

Journal of the American Chemical Society·2026
Same author

Serum Biomarkers in Bladder Cancer: NMR Metabolomics for Identification and Monitoring during Platinum-Based Therapy.

Oncology research·2026
Same author

Exclusion of CLIC5 as a Candidate Gene and Identification of NEFM as a Possible Novel Gene Correlated With Autosomal Recessive Pure Cerebellar Ataxia in a Highly Consanguineous Family.

Molecular genetics & genomic medicine·2026

A new algorithm calculates atom depth in complex molecules by considering molecular shape, improving predictions of molecular interactions and protein properties. This volume-based method offers better correlation with experimental data than traditional distance-based approaches.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Delineating atom-atom contacts, exposed surface, and binding sites is crucial for predicting molecular interactions.
  • Atom depth is an emerging descriptor for correlating protein structure with folding and function.
  • Existing methods for atom depth calculation, based on distances, often neglect the 3D molecular shape.

Purpose of the Study:

  • To develop and validate a novel algorithm for calculating atom depths that accounts for molecular shape.
  • To compare the efficacy of volume-based depth calculation against traditional distance-based methods.
  • To improve the correlation between structural descriptors and experimental data for proteins.

Main Methods:

  • Developed an algorithm to compute intersections between molecular volume and spheres centered on atoms.

Related Experiment Videos

  • Applied the algorithm to various proteins of different sizes and shapes.
  • Analyzed hen egg white lysozyme using H/D exchange rates and paramagnetic perturbations to compare depth calculation methods.

    • Main Results:

    • The proposed volume-based algorithm calculates atom depths considering molecular shape.
    • This new method shows improved correlations with experimental data compared to distance-based approaches.
    • The enhanced correlation is particularly notable for atoms near the protein surface.

    Conclusions:

    • The novel volume-based atom depth calculation method accurately reflects the 3D character of atomic positions within a molecular structure.
    • This approach provides a more reliable descriptor for understanding protein structure-function relationships and molecular interactions.
    • The algorithm offers a valuable tool for structural bioinformatics and molecular modeling.