Molecular dynamics simulation approach to investigate dynamic behaviour of system through the application of newtonian mechanics

Aman Chandra Kaushik, Ajay Kumar, Shiv Bharadwaj, Ravi Chaudhary, Shakti Sahi

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Molecular dynamics simulations have been successfully incorporated and evolved into a mature technique within a variety of pharmaceutical research programs to study the complex biological and chemical systems. Broadly used in modern drug design, molecular docking methods can be used effectively to understand the macromolecular structure-to-function relationships and ligand conformations adopted within the binding sites of macromolecular targets. Information gathered about the dynamic properties of ligand–receptor binding such as free energy by evaluating critical phenomena involved in the intermolecular recognition process. These results can be employed to shift the usual paradigm of structural bioinformatics from studying single structures to analyse conformational ensembles. Today, as a variety of docking algorithms are available, an understanding of advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this chapter is to examine the current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advancements in the field and role played by integration of structure-and ligand-based methods.

Original languageEnglish
Title of host publicationSpringerBriefs in Computer Science
PublisherSpringer
Pages33-36
Number of pages4
Edition9783319757315
DOIs
StatePublished - 1 Jan 2018
Externally publishedYes

Publication series

NameSpringerBriefs in Computer Science
Number9783319757315
Volume0
ISSN (Print)2191-5768
ISSN (Electronic)2191-5776

Keywords

  • Docking algorithms
  • Drug discovery
  • Ligand–receptor binding
  • Molecular dynamics simulations
  • Structural bioinformatics

ASJC Scopus subject areas

  • General Computer Science

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