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

Optimizing protein representations with information theory.

Julian Mintseris1, Zhiping Weng

  • 1Bioinformatics Program, Boston University, Boston MA 02215, USA. julianm@bu.edu

Genome Informatics. International Conference on Genome Informatics
|February 16, 2005
PubMed
Summary
This summary is machine-generated.

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

A linguistics-based algorithm for RBP motif and context discovery.

bioRxiv : the preprint server for biology·2026
Same author

Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity.

Nature structural & molecular biology·2026
Same author

A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions.

RNA (New York, N.Y.)·2026
Same author

Natural language-based representation and modeling of RBP binding.

bioRxiv : the preprint server for biology·2026
Same author

An expanded registry of candidate cis-regulatory elements.

Nature·2026
Same author

PsychENCODE at 10: From genomic maps to mechanistic insights in mental illness.

Neuron·2025
Same journal

Linear regression models predicting strength of transcriptional activity of promoters.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Sign: large-scale gene network estimation environment for high performance computing.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Docking-calculation-based method for predicting protein-RNA interactions.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Mechanism of cell cycle disruption by multiple p53 pulses.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

Database for crude drugs and Kampo medicine.

Genome informatics. International Conference on Genome Informatics·2012
Same journal

A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar.

Genome informatics. International Conference on Genome Informatics·2011
See all related articles

This study introduces a data-driven approach to protein representation, optimizing atom groupings for improved energetic insights. The findings reveal key differences and similarities in interactions during protein folding and binding.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Traditional protein representation methods rely on predefined physical, chemical, or biological criteria.
  • These methods impose existing structural understanding onto atom-typing schemes for protein folding and interactions.
  • A data-driven approach is needed to optimize protein representations.

Purpose of the Study:

  • To develop an optimized protein representation using information-theoretic techniques.
  • To analyze atom partitions from protein monomer and interface datasets.
  • To compare energetic concepts in protein folding versus binding.

Main Methods:

  • Utilized information-theoretic techniques to dissect protein datasets.
  • Analyzed atom partitions from protein monomer and protein interface datasets.

Related Experiment Videos

  • Determined optimized protein representations for a given alphabet size.

    • Main Results:

    • Achieved optimized protein representations consistent with protein energetics.
    • Identified greater importance of hydrophobic interactions in monomers versus polar/charged interactions in interfaces.
    • Observed striking similarity in atom partitions at alphabet size five between monomers and interfaces.

    Conclusions:

    • The data-driven method provides an optimized protein representation.
    • Energetic concepts governing protein folding and binding are broadly similar.
    • Findings have implications for advanced structural studies of proteins.