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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...

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Related Experiment Video

Updated: Jun 13, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

GRAPE: GRaphical Abstracted Protein Explorer.

Gregory Cipriano1, Gary Wesenberg, Tom Grim

  • 1Department of Computer Sciences, University of Wisconsin-Madison Madison, WI 53715, USA. gregc@cs.wisc.edu

Nucleic Acids Research
|May 14, 2010
PubMed
Summary
This summary is machine-generated.

We developed GRaphical Abstracted Protein Explorer (GRAPE), a web server simplifying protein surface analysis. GRAPE uses abstraction to highlight key features, aiding in understanding protein function.

Related Experiment Videos

Last Updated: Jun 13, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein surfaces, or surfaces of interaction, are crucial for understanding protein function.
  • The complexity of protein surface geometry and fields hinders detailed analysis and feature identification.

Purpose of the Study:

  • To introduce GRaphical Abstracted Protein Explorer (GRAPE), a novel web server for exploring abstracted protein representations.
  • To simplify the visualization of complex protein surfaces and their associated scalar fields.

Main Methods:

  • Developed a specialized algorithm to abstract macromolecular surfaces, reducing detail while preserving large-scale features.
  • Smoothed scalar fields like electrostatic potential and hydropathy to decrease visual complexity.
  • Integrated a 3D viewer for rapid comparison between traditional and abstracted molecular surface views.

Main Results:

  • GRAPE provides abstracted protein surface representations that reduce visual complexity.
  • The tool effectively preserves large-scale structural features and smoothed scalar field distributions.
  • Users can quickly assess molecular shape and surface field distributions through abstracted views.

Conclusions:

  • Abstracted protein views offer a complementary approach to traditional molecular surface analysis.
  • GRAPE facilitates faster assessment of protein shape and surface field properties.
  • The GRAPE web server is freely available for researchers to explore protein structures.