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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...
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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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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wwLigCSRre: a 3D ligand-based server for hit identification and optimization.

O Sperandio1, M Petitjean, P Tuffery

  • 1MTi, INSERM UMR-S973, Université Paris Diderot - Paris 7, F75013, Paris, France.

Nucleic Acids Research
|May 12, 2009
PubMed
Summary

The wwLigCSRre web server offers 3D molecular similarity screening for drug discovery. It aids in exploring compound families and scaffold hopping for Structure-Activity Relationship (SAR) projects.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Ligand-based screening is crucial for identifying novel drug candidates.
  • Exploring chemical similarity and scaffold hopping aids in lead optimization.
  • Existing tools may lack comprehensive libraries or integrated 3D similarity analysis.

Purpose of the Study:

  • To introduce the wwLigCSRre web server, a versatile online facility for 3D molecular similarity screening.
  • To facilitate the exploration of chemical similarity within compound families.
  • To assist in scaffold hopping and the optimization of hit molecules in Structure-Activity Relationship (SAR) studies.

Main Methods:

  • The wwLigCSRre server utilizes a 3D molecular similarity engine for ligand-based screening.
  • It combines geometrical and physicochemical information for similarity assessment.
  • The server allows screening against diverse focused libraries (Kinase, CNS, GPCR, etc.), DrugBank, and DSSTOX/Carcinogenic databases.

Main Results:

  • The web server provides a user-friendly interface for 3D similarity searches.
  • It enables the identification of novel compound scaffolds and potential drug leads.
  • Users can screen proprietary compound banks and download them for further analysis.

Conclusions:

  • wwLigCSRre serves as a valuable resource for computational drug discovery.
  • The tool supports lead identification and optimization through efficient 3D similarity analysis.
  • It enhances SAR studies by proposing alternative scaffolds and optimizing existing hits.