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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...

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:

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...

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...

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,...

Polymers: Molecular Weight Distribution

Polymers: Molecular Weight Distribution

For any given polymer, the weight average molecular weight (Mw) is higher than, if not equal to, the number average molecular weight (Mn). The only situation in which the weight average molecular weight and the number average molecular weight are equal is when a polymer consists only of chains with equal molecular weight. However, this never happens in a synthetic polymer, since it is difficult to control the polymerization process up to a molecular level with accuracy to a hundred percent.

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Related Experiment Video

Updated: Jun 21, 2025

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

DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression.

Tao Liu¹, Lena Simine¹

¹Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada.

Journal of Chemical Information and Modeling

|July 9, 2024

Summary

We developed DeltaGzip, a computational method to predict binding free energy for biopolymers and ligands. This approach uses short simulations and data compression to accurately estimate binding affinities, accelerating drug and biosensor design.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Area of Science:

Computational biology
Biophysics
Bioinformatics

Background:

Designing biosequences for biosensing and therapeutics is complex.
Computational modeling can accelerate design via virtual screening.
Current models lack flexibility or are computationally expensive.

Purpose of the Study:

To introduce DeltaGzip, a novel computational approach.
To evaluate binding free energy in biopolymer-ligand complexes.
To overcome limitations of existing prediction methods.

Main Methods:

Utilizing ultrashort equilibrium molecular dynamics simulations.
Applying Kolmogorov complexity for entropy evaluation.
Approximating entropy using the Gzip lossless compression algorithm.

Main Results:

DeltaGzip accurately predicts binding free energy.
Method validated on protein-ligand complexes.
Predictions align with Jarzynski equality and experimental data.

Conclusions:

DeltaGzip offers an efficient computational tool for biosequence design.
The method enhances prediction accuracy under various conditions.
Accelerates development of novel therapeutics and biosensors.