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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...
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 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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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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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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Protein-specific scoring method for ligand discovery.

I-Lin Lu1, Hsiuying Wang

  • 1Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 19, 2012
PubMed
Summary
This summary is machine-generated.

Developing protein-specific scoring functions enhances virtual screening accuracy in drug discovery. This approach improves ligand identification by tailoring energy term weights to individual protein targets, boosting hit rates.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Protein-based virtual screening is crucial for drug discovery, relying heavily on docking programs.
  • The accuracy of docking programs depends on scoring functions, which traditionally use generic or physically derived weights.
  • Existing scoring functions lack protein specificity, limiting their effectiveness.

Purpose of the Study:

  • To develop a protein-specific rescoring approach to improve virtual screening accuracy.
  • To enhance ligand selection by adjusting energy term weights based on protein characteristics.
  • To create a more effective tool for the drug discovery process.

Main Methods:

  • Proposed a protein-specific rescoring approach using linear regression analysis and outlier detection.
  • Adjusted the weights of energy terms within the scoring function.
  • Utilized the DOCK program as a model system and evaluated performance on the DUD dataset with 40 protein targets.

Main Results:

  • The protein-specific scoring function significantly improved enrichment factors for most of the 40 protein targets.
  • The method demonstrated substantial improvement when applied to a larger database.
  • The approach showed potential for enhancing other docking programs like GOLD and Glide.

Conclusions:

  • The developed protein-specific rescoring method effectively improves virtual screening performance.
  • This approach can be broadly applied to various docking programs and databases.
  • The method has the potential to significantly increase hit rates in virtual screening, benefiting drug discovery.