Related Experiment Video
Updated: Feb 24, 2026
08:49
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
1.4K
Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target
Leslie Regad1,2, Jean-Baptiste Chéron1,2,3, Dhoha Triki1,2
1Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France.
Plos One
|August 18, 2017
Summary
This study introduces SA-conf, a tool to analyze protein flexibility using multiple target conformations (MTCs). SA-conf quantifies structural variability, identifying key regions and sources of flexibility for better understanding protein function.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Protein flexibility is crucial for diverse biological functions, including partner binding.
- The Protein Data Bank (PDB) offers a vast resource of macromolecular structures, often with inherent redundancy.
- Analyzing multiple target conformations (MTCs) from various sources is key to exploring protein flexibility.
Purpose of the Study:
- To develop and validate an efficient tool, SA-conf, for analyzing protein structural variability.
- To explore the structural variability of three biological targets using MTC sets.
- To understand the sources and mechanisms of protein flexibility.
Main Methods:
- Development of the SA-conf tool for capturing and analyzing amino acid and local structure variability.
- Application of SA-conf to diverse MTC sets from PDB (NMR, crystallography) and homology models.
- Analysis of MTC sets obtained through dynamics approaches.
Main Results:
- SA-conf effectively quantifies structural variability within MTC sets.
- The tool accurately localizes structurally variable positions and regions within protein targets.
- Analysis revealed flexibility sources including binding partners, mutations, and intrinsic dynamics.
Conclusions:
- SA-conf is an effective tool for quantifying and localizing protein structural variability.
- Mining redundant structural data provides valuable insights into protein flexibility and interaction mechanisms.
- The study highlights the importance of considering MTCs for a comprehensive understanding of protein function.
More Related Videos
Related Concept Videos
01:49Conserved Binding Sites
5.2K
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...
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...
5.2K
00:49Ligand Binding and Linkage
5.7K
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...
5.7K