Related Experiment Video
Updated: Mar 5, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
16.1K
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.
Jianjiong Gao1, Andreas Prlic2, Chunxiao Bi2
1Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
Bioinformatics (Oxford, England)
|March 24, 2017
Summary
A new software tool, BioJava-ModFinder, identifies over 400 protein modifications in 3D structures from the Protein Data Bank (PDB). This tool enhances the RCSB PDB website, making modified protein structures searchable and visualized.
Area of Science:
- Structural Biology
- Bioinformatics
Background:
- Protein modifications are crucial for protein function and are extensively documented.
- Existing databases like PDB, RESID, and PSI-MOD contain valuable information on these modifications.
Purpose of the Study:
- To develop a novel software tool for systematically identifying protein modifications in 3D structures.
- To integrate this tool with the RCSB PDB web application for enhanced data accessibility.
Main Methods:
- Developed BioJava-ModFinder, a software tool for identifying protein modifications.
- Collected and curated information on over 400 modification types from PDB, RESID, and PSI-MOD.
- Categorized modifications into modified residues, attachment modifications, and cross-links.
Main Results:
- Identified over 30,000 PDB structures containing protein modifications.
- Integrated BioJava-ModFinder with the RCSB PDB web application.
- Added protein modification annotations to sequence diagrams and structure displays on RCSB PDB.
Conclusions:
- BioJava-ModFinder enables systematic identification and annotation of protein modifications in 3D structures.
- The integration with RCSB PDB significantly improves the discoverability and visualization of modified protein structures.
- This resource facilitates research into the roles of protein modifications in biological systems.
More Related Videos
05:57Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
Published on: April 26, 2024
939
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
2.7K
Related Concept Videos
01:24Protein Organization
9.9K
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....
The primary structure of a protein is its amino acid sequence....
9.9K
02:04Covalently Linked Protein Regulators
9.9K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
These groups modify specific amino acids in a protein....
9.9K
02:21Globular and Fibrous Proteins
47.8K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
47.8K
02:26Protein Networks
4.6K
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,...
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,...
4.6K
01:26Protein Modifications in the RER
7.3K
Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
Broadly, these modifications can be categorized into four main categories — glycosylation, formation of disulfide bonds, assembly of protein subunits, and specific proteolytic cleavages like removal of signal...
7.3K
02:47Protein Families
17.3K
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...
17.3K