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

PIDD: database for Protein Inter-atomic Distance Distributions.

Di Wu1, Feng Cui, Robert Jernigan

  • 1Program on Bioinformatics and Computational Biology, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Nucleic Acids Research
|December 8, 2006
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

Electricity generation from food wastes and microbial community structure in microbial fuel cells.

Bioresource technology·2013
Same author

Sex differences in the toxicity of polyethylene glycol-coated gold nanoparticles in mice.

International journal of nanomedicine·2013
Same author

Plasmon-enhanced photothermoelectric conversion in chemical vapor deposited graphene p-n junctions.

Journal of the American Chemical Society·2013
Same author

Rapid and sensitive detection of vinorelbine in the urine of tumor patients by capillary electrophoresis with tris(2,2'-bipyridyl)ruthenium(II)-based electrochemiluminescence assay.

Analytical sciences : the international journal of the Japan Society for Analytical Chemistry·2013
Same author

Synthesis and biological evaluation of 4-phenoxy-6,7-disubstituted quinolines possessing semicarbazone scaffolds as selective c-Met inhibitors.

Archiv der Pharmazie·2013
Same author

The effects of external electric field: creating non-zero first hyperpolarizability for centrosymmetric benzene and strongly enhancing first hyperpolarizability for non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2.

Journal of molecular modeling·2013
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Protein Inter-atomic Distance Distributions (PIDD) is a database for protein modeling. It analyzes inter-atomic distances from known structures to aid in protein structure determination and refinement.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Protein structure determination is crucial for understanding biological function.
  • Existing methods for protein modeling often rely on geometric constraints.
  • Statistical analysis of inter-atomic distances can provide valuable insights into protein structure.

Purpose of the Study:

  • To introduce the Protein Inter-atomic Distance Distributions (PIDD) database and system.
  • To provide a resource for analyzing protein inter-atomic distance distributions.
  • To facilitate distance-based protein modeling and structure refinement.

Main Methods:

  • Collected and analyzed statistical data of protein inter-atomic distances from the Protein Data Bank (PDB).
  • Developed a system for generating, caching, and displaying these distance distributions.

Related Experiment Videos

  • Implemented a web interface for user-friendly access and data retrieval.

    • Main Results:

    • The PIDD database hosts comprehensive statistical distributions of protein inter-atomic distances.
    • The system can generate, cache, and visualize these distributions for various distance types and ranges.
    • The collected data can be used to extract geometric restraints and mean-force potentials.

    Conclusions:

    • PIDD serves as a valuable resource for distance-based protein modeling.
    • The database supports protein structure determination, including NMR and comparative modeling.
    • PIDD offers a user-friendly platform for accessing and utilizing protein inter-atomic distance data.