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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Protein Folding01:22

Protein Folding

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and

Xin Deng1, Jianlin Cheng

  • 1Department of Computer Science, University of Missouri-Columbia, Columbia, MO 65211, USA.

BMC Bioinformatics
|December 16, 2011
PubMed
Summary

A new method, MSACompro, improves multiple sequence alignment accuracy by integrating predicted protein structural data. This bioinformatics tool enhances accuracy in tasks like protein function prediction and phylogenetic analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple Sequence Alignment (MSA) is fundamental to bioinformatics.
  • MSA is crucial for protein structure modeling, function prediction, and phylogenetic analysis.
  • Enhancing MSA accuracy is vital for advancing numerous bioinformatics fields.

Purpose of the Study:

  • To develop a novel method, MSACompro, for improving multiple sequence alignment accuracy.
  • To integrate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into MSA.

Main Methods:

  • Developed MSACompro, a novel posterior probability-based MSA method.
  • Incorporated predicted structural information (secondary structure, solvent accessibility, contact maps) derived solely from sequences.
  • Distinguished from methods using known tertiary structures.

Main Results:

  • MSACompro significantly improved multiple sequence alignment accuracy compared to leading tools lacking structural information.
  • Performance was comparable to state-of-the-art methods utilizing structural features and homologous sequences.
  • Benchmarking on BAliBASE, SABmark, and OXBENCH confirmed accuracy improvements.

Conclusions:

  • MSACompro is an efficient and reliable tool for multiple protein sequence alignment.
  • Effectively leverages predicted protein structural information to enhance MSA.
  • Software is publicly available for research use.