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

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.

M Tyagi1, P Sharma, C S Swamy

  • 1Laboratoire de Biochimie et Génétique Moléculaire, Bioinformatics Team, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France.

Nucleic Acids Research
|July 18, 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

Synthesis, crystal structure and Hirshfeld surface analysis of bis-[<i>N</i>-(4-chloro-benz-yl)-<i>N</i>-do-decyl-dithio-carbamato-κ<sup>2</sup> <i>S</i>,<i>S</i>']palladium(II).

Acta crystallographica. Section E, Crystallographic communications·2026
Same author

Comment on "efficacy of glucagon-like Peptide-1 receptor agonists in idiopathic intracranial hypertension: A systematic review and meta-analysis".

Journal of the neurological sciences·2026
Same author

Conservative management of intranasal tooth.

British dental journal·2026
Same author

THE IMPACT OF SLEEP ON PHYSICAL AND MENTAL HEALTH: IMPORTANCE OF HEALTHY SLEEP HABITS.

Georgian medical news·2023
Same author

Deciphering the role of Saliva in COVID 19: A global cross-sectional study on the knowledge, awareness and perception among dentists.

BMC oral health·2023
Same author

Decreased Brain Ventricular Volume in Psychiatric Inpatients with Serotonin Reuptake Inhibitor Treatment.

Chronic stress (Thousand Oaks, Calif.)·2022
Same journal

Cap 2'-O-methyltransferase CMTR2 regulates male meiosis independent of its methyltransferase activity.

Nucleic acids research·2026
Same journal

APE1 binds and processes abasic sites present in i-motif DNA and cooperates with PCBP1 in maintenance of telomeric stability.

Nucleic acids research·2026
Same journal

Acquisition of a novel restriction modification system regulates genetic flux and gene expression in the hypervirulent and globally disseminated CC17 lineage of group B Streptococcus.

Nucleic acids research·2026
Same journal

Trans-species microRNAs from the parasitic plant Cuscuta campestris specifically avoid loading onto self Argonautes.

Nucleic acids research·2026
Same journal

Neurochondrin promotes U5 snRNP maturation by regulating AAR2 release from PRPF8.

Nucleic acids research·2026
Same journal

Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.

Nucleic acids research·2026
See all related articles

Protein Blocks (PBs) enable protein 3D structure comparison by encoding them as 1D sequences. The Protein Block Expert (PBE) server facilitates this analysis and database mining.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Bioinformatics tools

Background:

  • Protein 3D structure analysis is crucial for understanding function.
  • Comparing protein structures computationally is challenging.
  • Existing methods may not efficiently handle large structural datasets.

Purpose of the Study:

  • To develop a novel methodology for protein structure comparison and analysis.
  • To encode protein 3D structures into 1D sequences using Protein Blocks (PBs).
  • To create a user-friendly server (PBE) for these analyses.

Main Methods:

  • Utilizing the 16 motifs of Protein Blocks (PBs) as a structural alphabet.
  • Encoding protein structures into sequences of PBs.
  • Applying dynamic programming with a substitution matrix for PB sequence alignment.

Related Experiment Videos

  • Implementing the methodology in the Protein Block Expert (PBE) server.

    • Main Results:

    • Developed a robust methodology for comparing protein structures via PB sequence alignment.
    • Created the Protein Block Expert (PBE) server with tools for structure transformation (PBE-T), pairwise comparison (PBE-ALIGNc), and database mining (PBE-ALIGNm).
    • Established a database (PBE-SAdb) of preprocessed PB sequences and alignments from the SCOP database.

    Conclusions:

    • The PBE server provides effective solutions for protein structure comparison and identification.
    • Encoding protein structures using PBs offers a new avenue for structural analysis and discovery.
    • The PBE server is freely accessible, promoting broader use in the research community.