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Related Concept Videos

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 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...
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins.

Kuan Pern Tan1, Raghavan Varadarajan, M S Madhusudhan

  • 1Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore.

Nucleic Acids Research
|May 18, 2011
PubMed
Summary

This study introduces DEPTH, a server that calculates protein residue depth and solvent-accessible surface area (SASA) to predict small molecule binding sites. The method accurately identifies ligand-binding cavities, aiding in drug discovery and protein functional annotation.

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Published on: January 26, 2024

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein residue depth quantifies atom burial and correlates with stability and functional sites.
  • Identifying small molecule binding cavities is crucial for drug discovery.
  • Existing methods for cavity prediction have limitations.

Purpose of the Study:

  • To develop and validate a computational server, DEPTH, for accurate calculation of residue depth and solvent-accessible surface area (SASA).
  • To demonstrate the utility of depth and SASA values in predicting small molecule ligand binding cavities in proteins.
  • To provide a user-friendly tool for structural analysis, aiding in drug discovery and protein functional annotation.

Main Methods:

  • The DEPTH server computes residue depth and SASA values from protein 3D structures (PDB format).
  • A prediction model was developed using depth-SASA pairs to estimate the likelihood of a residue forming part of a binding cavity.
  • Model parameters were calibrated on 900 high-resolution X-ray crystal structures and tested on 225 structures.

Main Results:

  • The DEPTH server accurately computes residue depth and SASA.
  • The method effectively predicts small molecule ligand binding cavities, with accuracy comparable to existing tools (Matthew's correlation coefficient ~0.4).
  • Predictions are visualized in 2D plots and 3D protein models, with user-adjustable parameters for different cavity sizes.

Conclusions:

  • The DEPTH server provides an accurate and accessible method for predicting protein binding cavities using residue depth and SASA.
  • This tool aids in structural analysis, site-directed mutagenesis, and small molecule docking.
  • DEPTH facilitates protein functional annotation and accelerates drug discovery efforts.