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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes.

Brian R King1, Suleyman Vural, Sanjit Pandey

  • 1Department of Computer Science, Bucknell University, One Dent Drive, Lewisburg, PA 17837, USA.

BMC Research Notes
|July 12, 2012
PubMed
Summary

We developed ngLOC, a new computational tool for predicting protein subcellular localization. This method accurately identifies protein locations in various species and is available as free software and a web server for research use.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein subcellular localization is crucial for understanding protein function.
  • Existing computational methods for predicting protein localization have limitations in availability and scope.
  • Many proteins shuttle between cellular compartments, necessitating methods that can predict multiple locations.

Purpose of the Study:

  • To present the ngLOC software package and web server for predicting protein subcellular localization.
  • To provide a robust and accessible tool for researchers to determine where proteins reside within cells.

Main Methods:

  • Utilized an n-gram-based Bayesian classifier (ngLOC).
  • Developed a method applicable to both prokaryotic and eukaryotic protein sequences.
  • Trained the generic method on diverse species and classes for broad applicability.

Main Results:

  • Achieved high prediction accuracy, ranging from 89.8% to 91.4% across species.
  • The tool predicts 11 distinct subcellular locations in plant and animal species.
  • ngLOC predicts 4 and 5 distinct locations for gram-positive and gram-negative bacteria, respectively.

Conclusions:

  • ngLOC is a versatile method adaptable to various species and protein classes.
  • The standalone software is freely available under GNU GPL for academic use.
  • An accessible web server for ngLOC is available at http://ngloc.unmc.edu.