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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...
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...

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PocketAlign a novel algorithm for aligning binding sites in protein structures.

Kalidas Yeturu1, Nagasuma Chandra

  • 1Bioinformatics Centre, Indian Institute of Science, Bangalore-560012, India.

Journal of Chemical Information and Modeling
|June 14, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces PocketAlign, a new algorithm for comparing protein binding sites. PocketAlign accurately maps structural similarities between sites, aiding in understanding protein function and drug interactions.

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Published on: April 3, 2026

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein similarity analysis is crucial for knowledge transfer and understanding function.
  • Comparing protein binding sites reveals functional similarities and predicts drug cross-reactivities.
  • Existing methods for binding site comparison have limitations, necessitating novel algorithms for large-scale and accurate analysis.

Purpose of the Study:

  • To develop a new algorithm, PocketAlign, for accurate structural superposition and comparison of protein binding sites.
  • To provide a web-service for researchers to perform binding site comparisons.
  • To offer insights into the reasons behind functional similarities between protein binding sites.

Main Methods:

  • PocketAlign encodes shape descriptors using geometric perspectives and chemical group classification.
  • It computes residue-wise pairings by comparing residue distribution patterns around each residue.
  • The algorithm uses a greedy approach to build mappings, evaluates them using various metrics, and ranks top alignments.

Main Results:

  • PocketAlign successfully generates structural superpositions of binding sites.
  • The method is validated for accuracy and sensitivity, outperforming existing tools in certain aspects.
  • It provides detailed residue and atomic level insights into binding site similarities.

Conclusions:

  • PocketAlign offers an advanced approach for protein binding site comparison, enhancing the understanding of ligand recognition.
  • The algorithm's ability to explore diverse alignment schemes improves the potential for capturing functional similarities.
  • PocketAlign serves as a valuable tool for bioinformatics research, facilitating drug discovery and protein function studies.