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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...
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 Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Phosphorylation01:02

Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
Phosphorylation01:02

Phosphorylation

The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Jun 7, 2026

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry
08:07

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Published on: July 26, 2019

Phosphate binding sites identification in protein structures.

Luca Parca1, Pier Federico Gherardini, Manuela Helmer-Citterich

  • 1Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.

Nucleic Acids Research
|October 27, 2010
PubMed
Summary
This summary is machine-generated.

A new computational method, Pfinder, can predict phosphate-binding sites in proteins. This tool aids in understanding protein function and designing new drugs by identifying where phosphate groups attach.

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PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions
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PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

Published on: July 27, 2017

Related Experiment Videos

Last Updated: Jun 7, 2026

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry
08:07

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Published on: July 26, 2019

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions
10:58

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

Published on: July 27, 2017

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • Phosphate-containing molecules, including nucleotides, are crucial in nearly half of known protein structures.
  • Existing computational methods can identify metal ion or carbohydrate binding sites, but none specifically predict phosphate-binding sites.

Purpose of the Study:

  • To develop and present Pfinder, a novel computational method for predicting phosphate-binding sites in proteins.
  • To enable the identification of binding sites for phosphate ions and phosphate groups within non-peptide ligands in proteins with known structures.

Main Methods:

  • Pfinder utilizes the Query3D local structural comparison algorithm.
  • The method scans protein structures for specific structural motifs known to bind phosphate groups.
  • The algorithm was tested on 52 proteins with available apo (unbound) and holo (bound) forms.

Main Results:

  • Pfinder achieved at least one correct prediction in 63% of holo structures and 62% of apo structures.
  • The method demonstrates efficacy in identifying phosphate-binding sites even in unbound protein conformations.

Conclusions:

  • Pfinder is an effective tool for predicting phosphate-binding sites in proteins.
  • Its ability to function on unbound structures makes it valuable for protein functional annotation.
  • Pfinder can complement existing docking and drug design methodologies.