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Related Concept Videos

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.
Statistical Package for the Social Sciences (SPSS)01:22

Statistical Package for the Social Sciences (SPSS)

The Statistical Package for the Social Sciences, or SPSS, is a data management and analysis software suite. Developed by SPSS Inc. in 1968 and acquired by IBM in 2009, this tool was initially designed for social science data analysis, evolving to serve a wider range of disciplines. It was later renamed to Statistical Product and Service Solutions.
SPSS streamlines the process from data preparation to analysis and reporting. It is characterized by its user-friendly interface, which conceals...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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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...
Statgraphics01:10

Statgraphics

Statgraphics is a comprehensive statistical software suite designed for both basic and advanced data analysis. Originating in 1980 at Princeton University under Dr. Neil W. Polhemus, it was one of the pioneering tools for statistical computing on personal computers, with its public release in 1982 marking an early milestone in data science software. Over the years, it has evolved into a robust platform for data science, offering tools for regression analysis, ANOVA, multivariate statistics,...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Protein structural statistics with PSS.

Thomas Gaillard1, Benjamin B L Schwarz, Yassmine Chebaro

  • 1Laboratoire de Biochimie, UMR 7654 CNRS, Ecole Polytechnique , 91128 Palaiseau Cedex, France.

Journal of Chemical Information and Modeling
|August 21, 2013
PubMed
Summary
This summary is machine-generated.

Protein Structural Statistics (PSS) is a new Perl program that automates the comparison of multiple protein structures. It provides essential structural statistics and analysis for large datasets in bioinformatics.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Characterizing protein structure ensembles is crucial in structural biology and bioinformatics.
  • The growing number of available protein structures necessitates automated tools for large-scale structural comparison.

Purpose of the Study:

  • To introduce Protein Structural Statistics (PSS), a command-line program for automated structural statistics calculation.
  • To provide a user-friendly and flexible tool for comparing multiple protein structures and analyzing structural variability.

Main Methods:

  • Developed PSS as a Perl-based command-line program for Unix-like environments.
  • Implemented functionalities for multiple sequence alignments, structure superpositions, and Cartesian/dihedral coordinate statistics.
  • Integrated cluster analysis and automated generation of HTML reports with summaries, figures, tables, and hyperlinks.

Main Results:

  • PSS offers an automated approach to compare multiple protein structures.
  • The program integrates diverse structural analyses, simplifying access to specialized functionalities.
  • Generated HTML reports provide a convenient summary of results for biological problem-solving.

Conclusions:

  • PSS is a valuable, extendable, and open-source tool for structural bioinformatics.
  • Its automated features facilitate the analysis of large protein structure ensembles.
  • The program's flexibility and ease of use aid in addressing pertinent biological questions.