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Related Concept Videos

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...
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.
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Overview of Functional Groups01:19

Overview of Functional Groups

Functional groups are a group of atoms with characteristic properties, which when linked to the carbon skeleton of a molecule, alter the properties of that molecule. For example, certain functional groups will make a molecule hydrophilic, whereas others will make them hydrophobic. These functional groups are an indispensable part of organic chemistry and important components of biological molecules, such as carbohydrates, proteins, lipids, and nucleic acids. Each functional group is a unique...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Published on: June 17, 2012

PocketAnnotate: towards site-based function annotation.

Praveen Anand1, Kalidas Yeturu, Nagasuma Chandra

  • 1Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India.

Nucleic Acids Research
|May 24, 2012
PubMed
Summary
This summary is machine-generated.

PocketAnnotate is a new computational pipeline for protein functional annotation using binding site analysis. It helps infer protein function from structure, especially when sequence data is insufficient.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Functional annotation of proteins is crucial for understanding biological processes.
  • Sequence and fold-level analyses can be insufficient for inferring protein function.
  • Structure-based approaches offer complementary insights into protein roles.

Purpose of the Study:

  • To introduce PocketAnnotate, a computational pipeline for functional annotation of proteins based on their binding sites.
  • To develop a novel method for generating a non-redundant database of binding sites.
  • To enable structure-based functional inference for proteins with unknown functions.

Main Methods:

  • Integration of three algorithms: PocketDepth (binding site prediction), PocketMatch (binding site comparison), and PocketAlign (binding site alignment).
  • Development of a novel scheme for rapid generation of a non-redundant binding site database.
  • Real-time matching of input protein binding sites against the database and alignment with promising hits.

Main Results:

  • PocketAnnotate successfully identifies putative ligand-binding sites in protein structures.
  • The pipeline facilitates rapid comparison and alignment of binding sites.
  • It enables the prediction of potential ligands for a given protein structure.
  • Analysis of proteins with unknown functions from the Protein Data Bank was performed.

Conclusions:

  • PocketAnnotate provides a valuable tool for structure-based functional inference.
  • The pipeline is particularly useful for proteins lacking clear functional annotation from sequence or fold analysis.
  • PocketAnnotate contributes to advancing our understanding of protein function through structural insights.