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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...
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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Pre-docking filter for protein and ligand 3D structures.

Alisa Wilantho1, Sissades Tongsima, Ekachai Jenwitheesuk

  • 1National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klongluang, Pathumtani 12120, Thailand.

Bioinformation
|March 4, 2009
PubMed
Summary
This summary is machine-generated.

Filtering compounds before virtual drug screening can significantly speed up the process. Analyzing ligand volume and flexibility helps identify molecules with high binding affinity, reducing computational costs.

Keywords:
binding affinitydocking filterligand volumeprotein binding sitevirtual drug screening

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • Virtual drug screening (VDS) is computationally intensive, requiring significant resources for binding affinity calculations.
  • Millions of chemical compounds are available for VDS, necessitating efficient methods to prioritize candidates.
  • Identifying and removing low-affinity ligands early can accelerate the VDS procedure.

Purpose of the Study:

  • To develop and evaluate a pre-docking filtering strategy to enhance the efficiency of virtual drug screening.
  • To investigate the relationship between ligand properties (volume, rotatable bonds) and binding affinity.
  • To reduce the computational burden of VDS by filtering out unlikely binders.

Main Methods:

  • Performed protein-ligand docking for 6353 ligands against 21 protein X-ray crystal structures.
  • Ranked docked ligands by calculated binding affinities.
  • Analyzed the characteristics (volume, rotatable bonds) of top-ranked and bottom-ranked ligand sets.

Main Results:

  • Top-ranked ligands exhibited volumes and rotatable bond counts similar to those in crystal structures and matched binding site volumes.
  • Bottom-ranked ligands were often too large to fit or too small for specific, high-affinity binding.
  • Ligand volume and flexibility correlated with binding site characteristics and affinity.

Conclusions:

  • A pre-docking filter considering binding site and ligand shape/volume can effectively remove low-affinity compounds.
  • This filtering approach significantly increases the speed of virtual drug screening.
  • Optimizing ligand selection prior to docking improves the efficiency of drug discovery pipelines.