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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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...
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: May 15, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Mapping small molecule binding data to structural domains.

Felix A Kruger1, Raghd Rostom, John P Overington

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.

BMC Bioinformatics
|January 4, 2013
PubMed
Summary
This summary is machine-generated.

This study maps small molecule binding to specific protein structural domains (Pfam) in the ChEMBL database. This approach enhances drug discovery by organizing bioactivity data and identifying potential drug targets.

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Last Updated: May 15, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Drug Discovery

Background:

  • Large-scale bioactivity data aids drug discovery but faces limitations in target interaction sparsity and complex target-bioactivity relationships.
  • Bioinformatics tools struggle to clearly link bioactivity to specific protein targets.
  • Indexing protein targets by their ligand-binding structural domains offers a novel approach.

Purpose of the Study:

  • To develop and validate a heuristic method for mapping small molecule ligand binding to Pfam domains within protein targets.
  • To enhance the annotation of bioactivity data by linking it to specific structural domains.
  • To facilitate drug discovery by improving target identification and assessment.

Main Methods:

  • A heuristic was developed to map small molecule binding sites to Pfam domains.
  • Ligand-protein interactions from the ChEMBL database were mapped to Pfam-A domains.
  • Validation was performed against Uniprot entries and wwPDB crystallographic structures.

Main Results:

  • The mapping revealed that most ChEMBL assay targets bind ligands via a few prevalent Pfam domains.
  • A significant portion of Pfam domains show no established role in current ligand binding.
  • The heuristic demonstrated approximately 90% accuracy in mapping ligand binding to the correct domain.

Conclusions:

  • Small molecule binding has been successfully mapped to Pfam-A domains in the ChEMBL database.
  • This mapping enriches bioactivity data annotation and groups activity classes by protein domains.
  • The approach is valuable for drug discovery, aiding in target extrapolation and assessment for screening studies.