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Conserved Binding Sites

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...

Ligand Binding Sites

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 Interfaces

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...

The Equilibrium Binding Constant and Binding Strength

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:

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

Protein-Drug Binding: Determination Methods

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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Related Experiment Video

Updated: Jun 21, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.

Magdalena A Krupa¹, Paweł Krupa²

¹Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.

Methods in Molecular Biology (Clifton, N.J.)

|July 10, 2024

Summary

Molecular docking predicts molecule orientations. Physics-based methods are reliable for scarce data, while knowledge- or template-based methods are efficient for abundant data.

Keywords:

Carbon nanoparticles Force fields Fullerenes Genetic algorithms Knowledge-based docking methods Molecular dynamics Physics-based docking methods Proteins and peptides Template-based docking methods UNRES

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Last Updated: Jun 21, 2025

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational chemistry
Structural biology
Biophysics

Background:

Molecular docking predicts the relative orientation of molecules.
Methods include physics-based, knowledge-based, and template-based approaches.
Usability depends on molecule type, size, and available structural information.

Purpose of the Study:

Compare and discuss various docking methods.
Highlight limitations such as computational cost and data availability.
Emphasize physics-based methods for systems with limited structural data.

Main Methods:

Discusses knowledge-based, template-based, and physics-based docking algorithms.
Compares their accuracy and computational efficiency.
Focuses on the UNRES coarse-grained model for specific applications.

Main Results:

Knowledge- and template-based methods reduce cost and maintain accuracy with sufficient data.
Physics-based methods are more reliable when structural information is scarce.
Demonstrates usability with examples of protein-protein, protein-peptide, and protein-fullerene docking.

Conclusions:

The choice of docking method depends on data availability and computational resources.
Physics-based methods offer reliability in data-scarce scenarios.
The UNRES model provides a framework for diverse docking applications.