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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...
Drug-Receptor Bonds01:25

Drug-Receptor Bonds

Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
In...
Classification of Neurotransmitters01:30

Classification of Neurotransmitters

Neurotransmitters play a crucial role in the communication between neurons in the autonomic nervous system. Neurons in the autonomic nervous system can be cholinergic or adrenergic depending on the neurotransmitters synthesized. Cholinergic neurons use acetylcholine as their primary neurotransmitter. This includes all the preganglionic fibers of the sympathetic and pre- and postganglionic fibers of the parasympathetic nervous systems. In addition, neurons of the somatic nervous system also use...

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Updated: May 28, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

NNScore 2.0: a neural-network receptor-ligand scoring function.

Jacob D Durrant1, J Andrew McCammon

  • 1Department of Chemistry and Biochemistry and §Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA. jdurrant@ucsd.edu

Journal of Chemical Information and Modeling
|October 25, 2011
PubMed
Summary
This summary is machine-generated.

NNScore 2.0, a new neural-network scoring function, enhances computational ligand identification by considering more binding characteristics. This open-source tool provides accurate affinity predictions, validating neural networks against state-of-the-art docking programs.

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Last Updated: May 28, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • NNScore is a neural-network-based scoring function for identifying small-molecule ligands.
  • Previous applications were limited, necessitating further validation.

Purpose of the Study:

  • To confirm the effectiveness of neural-network scoring functions compared to leading docking programs like AutoDock and AutoDock Vina.
  • To introduce NNScore 2.0, an improved neural-network scoring function.

Main Methods:

  • Development and validation of NNScore 2.0, a neural-network scoring function.
  • Comparison of NNScore 2.0 performance against established docking programs.
  • Implementation of NNScore 2.0 as an open-source Python script.

Main Results:

  • NNScore 2.0 considers a broader range of binding characteristics than the original NNScore.
  • NNScore 2.0 outputs a pK(d) estimate, unlike the binary classification of NNScore 1.0.
  • The study provides further validation for neural-network scoring functions in ligand identification.

Conclusions:

  • Neural-network scoring functions are effective for computational ligand identification.
  • NNScore 2.0 offers an advanced and accessible tool for predicting ligand-protein binding affinity.
  • The open-source nature of NNScore 2.0 facilitates its adoption and further research.