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Protein Networks

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 Networks

Protein Networks

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Proteomics

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...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

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Related Experiment Video

Updated: Nov 6, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Structural genomics and the Protein Data Bank.

Karolina Michalska¹, Andrzej Joachimiak²

¹Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA; Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.

The Journal of Biological Chemistry

|May 6, 2021

Summary

Structural genomics emerged to bridge gaps in protein data. This field developed pipelines to determine structures of novel proteins, advancing molecular and structural biology.

Keywords:

Protein Data Bank X-ray crystallography databases structural biology structural genomics

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Area of Science:

Structural biology
Genomics
Biochemistry

Background:

Structural genomics emerged to address the growing divergence between genomic, functional, and structural data.
International programs leveraged genomic data to assess structure determination feasibility for novel protein families.

Observation:

Structural genomics developed pipelines for structure determination, applying them to uncharacterized proteins and human pathogens.
Key advances were needed in protein production and rapid de novo structure solution.

Findings:

Experimental 3D protein models were rapidly disseminated, aiding further structure determination and functional analysis.
Improvements in experimental methods and databases accelerated progress in molecular and structural biology.

Implications:

The Protein Data Bank (PDB) was central to coordinating structural genomics efforts and the broader structural biology community.
The PDB facilitated the development of standards and validation tools, ensuring high-quality structural data.