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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
Protein Families02:47

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 locations, protein...

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Related Experiment Video

Updated: May 21, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.

Ya-Nan Zhang1, Dong-Jun Yu, Shu-Sen Li

  • 1Department of Automation, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.

BMC Bioinformatics
|June 2, 2012
PubMed
Summary

We developed a new method to predict protein binding sites for Adenosine-5'-triphosphate (ATP). This approach combines sequence and structural features for accurate identification of functional residues in protein-ATP complexes.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Adenosine-5'-triphosphate (ATP) is a crucial nucleotide involved in numerous cellular processes as a coenzyme.
  • Understanding protein-ATP interactions is vital for elucidating protein function and complex mechanisms.

Purpose of the Study:

  • To propose a novel framework for accurately predicting protein residues that bind to ATP.
  • To enhance the understanding of protein-ATP binding site characteristics.

Main Methods:

  • Integration of sequence evolutional information.
  • Application of bi-profile sampling for multi-view sequential features.
  • Inclusion of sequence-derived structural features.

Main Results:

  • The proposed protocol demonstrates high prediction performance on benchmark datasets.
  • Identified distinct structural characteristics of ATP binding sites, including low solvent accessibility and preference for secondary structure junctions.
  • Performance is sensitive to training dataset balance and benefits from increased scale.

Conclusions:

  • The novel framework effectively predicts protein-ATP binding sites.
  • Structural features offer significant insights into the nature of these binding interactions.
  • Dataset scale and balance are critical factors for optimizing prediction accuracy.