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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Unified Aedes aegypti Protein Resource Database (UAAPRD): An Integrated High-Throughput In Silico Platform for

Anagha S Setlur1, Vidya Niranjan2, Chandrashekar Karunakaran1

  • 1Department of Biotechnology, RV College of Engineering affiliated to Visvesvaraya Technological University (VTU), Belagavi, 590018, India.

Molecular Biotechnology
|July 23, 2024
PubMed
Summary

This study introduces UAAPRD, a new database of Aedes aegypti mosquito proteins, aiding the development of novel insecticides and disease control strategies by identifying drug targets.

Keywords:
Aedes aegyptiDatabaseEvolutionary analysisModeling and validationMySQLPharmacophore models

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Area of Science:

  • * Vector biology and bioinformatics.
  • * Mosquito genomics and proteomics.
  • * Drug discovery and molecular modeling.

Background:

  • * Current research on Aedes aegypti focuses on repellents, neglecting unexplored proteomic targets for disease control.
  • * High-throughput data generation poses accessibility and usability challenges for researchers.
  • * A centralized database is needed to consolidate information on Aedes aegypti proteins, functions, and structures.

Purpose of the Study:

  • * To scrutinize key Aedes aegypti proteins for potential small molecule targeting.
  • * To model protein structures, identify druggable sites, and simulate molecular dynamics.
  • * To establish the UAAPRD database for accessible protein information and drug screening.

Main Methods:

  • * Protein structure modeling using RaptorX.
  • * Druggable binding site identification with BiteNet.
  • * Model validation via Ramachandran plots and 50-ns molecular dynamics simulations in Schrodinger Maestro.
  • * Analysis of ~18k Aedes aegypti proteome proteins, focusing on circadian rhythm, blood feeding, and metabolism.

Main Results:

  • * Development of UAAPRD, a MySQL database containing data on 309 modeled and simulated Aedes aegypti proteins.
  • * The database includes previously unmodeled and un-simulated mosquito proteins.
  • * UAAPRD provides access to protein data, evolutionary analysis, visualization, and drug screening requests.

Conclusions:

  • * UAAPRD offers a valuable resource for researchers studying Aedes aegypti.
  • * The database facilitates the identification of novel drug targets for vector control.
  • * This work contributes to developing more effective strategies against mosquito-borne diseases.