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Methods in molecular biology (Clifton, N.J.)
2024;2780 91-106.

Molecular Dynamics Simulations in Protein-Protein Docking.

Dominika Cie��lak, Ivo Kabelka, Damian Bartuzi
Author Information
  1. Dominika Cie��lak: Laboratory of Plant Protein Phosphorylation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
  2. Ivo Kabelka: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
  3. Damian Bartuzi: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. damian.bartuzi@icm.uu.se.
PMID: 38987465 DOI: 10.1007/978-1-0716-3985-6_6

Abstract

Concerted interactions between all the cell components form the basis of biological processes. Protein-protein interactions (PPIs) constitute a tremendous part of this interaction network. Deeper insight into PPIs can help us better understand numerous diseases and lead to the development of new diagnostic and therapeutic strategies. PPI interfaces, until recently, were considered undruggable. However, it is now believed that the interfaces contain "hot spots," which could be targeted by small molecules. Such a strategy would require high-quality structural data of PPIs, which are difficult to obtain experimentally. Therefore, in silico modeling can complement or be an alternative to in vitro approaches. There are several computational methods for analyzing the structural data of the binding partners and modeling of the protein-protein dimer/oligomer structure. The major problem with in silico structure prediction of protein assemblies is obtaining sufficient sampling of protein dynamics. One of the methods that can take protein flexibility and the effects of the environment into account is Molecular Dynamics (MD). While sampling of the whole protein-protein association process with plain MD would be computationally expensive, there are several strategies to harness the method to PPI studies while maintaining reasonable use of resources. This chapter reviews known applications of MD in the PPI investigation workflows.

Keywords

CG-MD Coarse-graining Enhanced sampling Gaussian-accelerated Molecular Dynamics Metadynamics Molecular docking PPI Protein���protein docking Protein���protein interactions Molecular dynamics

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MeSH Term

Molecular Dynamics Simulation
Molecular Docking Simulation
Proteins
Protein Binding
Protein Interaction Mapping
Protein Conformation
Humans
Software
Computational Biology

Chemicals

Proteins
Journal Article

Word Cloud

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