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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...
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...
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...
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...
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...

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
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Fpocket: an open source platform for ligand pocket detection.

Vincent Le Guilloux1, Peter Schmidtke, Pierre Tuffery

  • 1ICOA - Institut de chimie organique et analytique - UMR CNRS 6005, Div. of chemoinformatics and molecular modeling, University of Orléans, Orléans, France. vincent.le-guilloux@univ-orleans.fr

BMC Bioinformatics
|June 3, 2009
PubMed
Summary

Fpocket is a new open-source tool for detecting protein pockets, crucial for structure-based virtual screening (SBVS) in drug discovery. It accurately identifies binding sites, outperforming existing methods and offering a fast, stable platform for further research.

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
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Parallel Interrogation of β-Arrestin2 Recruitment for Ligand Screening on a GPCR-Wide Scale using PRESTO-Tango Assay
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Parallel Interrogation of β-Arrestin2 Recruitment for Ligand Screening on a GPCR-Wide Scale using PRESTO-Tango Assay

Published on: March 10, 2020

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Virtual screening (VS) methods are established for identifying drug candidates.
  • Structure-based VS (SBVS) requires accurate protein pocket identification for compound docking.
  • Developing robust methods for detecting pockets and cavities on protein surfaces is an active research area.

Purpose of the Study:

  • To introduce Fpocket, an open-source software package for protein pocket detection.
  • To provide a computational tool that enhances the efficiency and accuracy of structure-based virtual screening.

Main Methods:

  • Fpocket utilizes Voronoi tessellation and alpha spheres, built upon the Qhull library.
  • The software is implemented in C, featuring a modular design with core functions.
  • It includes three main programs: Fpocket for identification, Tpocket for benchmarking, and Dpocket for descriptor collection.

Main Results:

  • Fpocket achieves high accuracy, detecting 94% of pockets in holo proteins and 92% in apo proteins within the top three ranked pockets.
  • The method outperforms existing standards in pocket detection accuracy.
  • Fpocket demonstrates faster performance compared to other established methods.

Conclusions:

  • Fpocket offers a rapid, open-source, and stable foundation for protein pocket detection research.
  • It facilitates efficient pocket descriptor extraction and supports drugability prediction.
  • The software is freely available under the GNU GPL license.