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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...
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...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

CScore: a simple yet effective scoring function for protein-ligand binding affinity prediction using modified CMAC

Xuchang Ouyang1, Stephanus Daniel Handoko, Chee Keong Kwoh

  • 1BioInformatics Research Centre, School of Computer Engineering, Nanyang Technological University, 639798, Singapore. xouyang1@e.ntu.edu.sg

Journal of Bioinformatics and Computational Biology
|December 7, 2011
PubMed
Summary
This summary is machine-generated.

CScore, a novel data-driven scoring function, accurately predicts protein-ligand binding affinity. This computational method shows improved performance over existing scoring functions, aiding drug design.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-ligand docking is crucial for drug design, identifying binding modes and affinities.
  • Current scoring functions excel at predicting binding modes but struggle with accurate binding affinity prediction.

Purpose of the Study:

  • To introduce CScore, a data-driven scoring function utilizing a modified Cerebellar Model Articulation Controller (CMAC) learning architecture.
  • To evaluate CScore's accuracy in predicting protein-ligand binding affinities.

Main Methods:

  • Developed CScore, a scoring function based on a modified CMAC learning architecture.
  • Benchmarked CScore's performance using correlation (R) and root-mean-square error (RMSE) against experimental binding affinities.
  • Employed independent dataset testing and leave-cluster-out validation approaches.

Main Results:

  • CScore achieved R = 0.7668 and RMSE = 1.4540 on an independent dataset, outperforming other tested scoring functions.
  • Leave-cluster-out validation showed competitive, though variable, performance across different clusters.
  • Target-specific CScore models yielded superior results (R = 0.8237, RMSE = 1.0872) when trained on smaller, relevant datasets.

Conclusions:

  • CScore demonstrates accurate binding affinity prediction capabilities, driven by machine learning and large datasets.
  • Performance of CScore is enhanced with sufficient and relevant data, indicating potential for future improvements.
  • The growth of public structural data supports further refinement of data-driven scoring schemes like CScore.