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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...
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...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PocketMatch: a new algorithm to compare binding sites in protein structures.

Kalidas Yeturu1, Nagasuma Chandra

  • 1Bioinformatics Centre and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India. ykalidas@gmail.com

BMC Bioinformatics
|December 19, 2008
PubMed
Summary
This summary is machine-generated.

We developed PocketMatch, a new algorithm for comparing protein binding sites. It accurately identifies similarities using shape and chemical properties, enabling high-throughput analysis for biological research.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Protein similarity identification is crucial in biology, often relying on sequence or structural fold comparisons.
  • Functional similarities may be hidden in substructures, particularly at protein binding sites.
  • Current methods for binding site comparison lack sensitivity and high-throughput capabilities.

Purpose of the Study:

  • To develop a novel algorithm for sensitive, accurate, and high-throughput comparison of protein binding sites.
  • To address the limitations of existing analytical tools for inferring functional similarities from binding site data.

Main Methods:

  • Introduced PocketMatch, an algorithm representing binding sites using distance lists that capture shape and chemical properties.
  • Employed an incremental alignment method to score and compare binding sites, generating PocketMatch Scores (PMScores).
  • Conducted comprehensive sensitivity analyses, validation studies, and comparisons with existing algorithms.

Main Results:

  • PocketMatch compares binding sites in a frame-invariant manner, achieving high sensitivity.
  • Perturbation studies confirmed that chance similarities are virtually non-existent.
  • Combined shape and chemical nature information is essential for discriminating diverse binding sites.

Conclusions:

  • PocketMatch provides an accurate, efficient, and high-throughput method for binding site comparison.
  • The algorithm's simplistic representation combined with its alignment strategy enables sensitive binding site comparisons.
  • PocketMatch is computationally efficient, with a single comparison taking approximately 1/250th of a second.