Related Experiment Video
Updated: Jan 20, 2026
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery
Indrani Bera1, Pavan V Payghan2,3
1Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, United States.
Background:
Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process.
Objective:
The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design.
Method:
This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained.
Results:
This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations.
Conclusion:
The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.
More Related Videos
Related Concept Videos
08:49Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
15:05Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
05:57Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
06:37Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
10:29Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
12:03Dynamics of Structures
It is rare nowadays that a whole year goes by without a major earthquake event wreaking havoc somewhere around the world. In some cases, like the 2005 Banda Ache earthquake in Indonesia, the damage involved large geographic areas and casualties in the six figures. In general, the number and intensity of earthquakes is not increasing, however, the vulnerability of the built environment is...