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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...
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...
The Equilibrium Binding Constant and Binding Strength02:18

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:
The Equilibrium Binding Constant and Binding Strength02:18

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:
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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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Published on: July 25, 2013

A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions.

Yingtao Liu1, Zhijian Xu, Zhuo Yang

  • 1Drug Discovery and Design Center, CAS Key Laboratory of Receptor Structure and Function, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China, ytliu@mail.shcnc.ac.cn.

Journal of Molecular Modeling
|September 28, 2013
PubMed
Summary

A new scoring function, XBPMF, was developed to accurately predict halogen bonding interactions in protein-ligand complexes. This knowledge-based function improves upon existing methods for molecular docking and lead optimization.

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Protein Target Prediction and Validation of Small Molecule Compound
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Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Halogen bonding is a crucial non-covalent interaction in molecular recognition.
  • Existing scoring functions often fail to accurately characterize halogen bonding.
  • Improved prediction of these interactions is vital for drug design.

Purpose of the Study:

  • To develop a novel knowledge-based scoring function, XBPMF, specifically for predicting halogen bonding.
  • To evaluate the performance of XBPMF against established scoring functions.
  • To provide a practical tool for high-throughput virtual screening of halogen-containing compounds.

Main Methods:

  • Developed XBPMF using an iterative method and pairwise potentials derived from Protein Data Bank complexes.
  • Utilized two-dimensional pairwise potentials to capture distance and angle profiles of halogen bonding.
  • Compared XBPMF's performance (docking, ranking, scoring power) against six widely used scoring functions.

Main Results:

  • XBPMF demonstrated moderate predictive power for protein-ligand interactions.
  • Two-dimensional potentials were superior to one-dimensional potentials for characterizing halogen bonding.
  • XBPMF showed satisfactory performance for systems with typical halogen bonds.

Conclusions:

  • XBPMF is the first halogen bonding scoring function independent of dummy atoms.
  • The function is practical for high-throughput virtual screening.
  • XBPMF is a valuable tool for studying halogen bonding in molecular docking and lead optimization.