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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Updated: Sep 28, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features.

Hugo Schweke1,2, Marie-Hélène Mucchielli3,4, Nicolas Chevrollier5

  • 1Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France.

Journal of Chemical Information and Modeling
|March 29, 2022
PubMed
Summary
This summary is machine-generated.

SURFMAP is a new software for protein surface analysis. It creates 2D maps of protein features, aiding in visual and quantitative comparisons of homologous proteins.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Two-dimensional (2D) representation of protein surfaces is a valuable technique for molecular cartography and protein surface analysis.
  • Current methods may lack efficiency or ease of use for automated analysis of diverse protein surface features.

Purpose of the Study:

  • To introduce SURFMAP, a novel, free, standalone software for automated 2D projection of protein surface features.
  • To enable both visual and quantitative analysis of protein surface characteristics.

Main Methods:

  • SURFMAP utilizes three distinct "equal-area" projection methods to preserve area measures during 2D mapping.
  • The software projects predefined surface features (electrostatic potential, hydrophobicity, stickiness, surface relief) and custom descriptors from PDB temperature factor columns.
  • Automated projection and generation of both visual 2D maps and quantitative data files.

Main Results:

  • SURFMAP provides fast and automated generation of 2D protein surface maps.
  • The software facilitates easy visual analysis of protein surface features.
  • Generated text files allow for straightforward quantitative comparison of 2D maps, particularly for homologous proteins.

Conclusions:

  • SURFMAP offers an efficient and user-friendly tool for molecular cartography and protein surface analysis.
  • The software enhances the ability to visually and quantitatively compare protein surfaces.
  • SURFMAP is a valuable resource for researchers in structural biology and computational biochemistry.