Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

By Veronica Salmaso, Stefano Moro. 2018

553 citations recorded by the source corpus.

Computational techniques have been applied in the drug discovery pipeline since the 1980s. Given the low computational resources of the time, the first molecular modeling strategies relied on a rigid view of the ligand-target binding process. During the years, the evolution of hardware technologies has gradually allowed simulating the dynamic nature of the binding event. In this work, we present an overview of the evolution of structure-based drug discovery techniques in the study of ligand-target recognition phenomenon, going from the static molecular docking toward enhanced molecular dynamics strategies.

Subfields: Computational Theory and Mathematics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Rodrigo Vargas Honorato
2. Tatu Pantsar
3. Alexandre M. J. J. Bonvin
4. Giulio Rastelli
5. Luca Pinzi

In Molecular Biology

1. Rodrigo Vargas Honorato
2. Tatu Pantsar
3. Alexandre M. J. J. Bonvin
4. Giulio Rastelli
5. Luca Pinzi
6. M. V. van Dijk
7. Zeynep Kurkcuoglu
8. João P. G. L. M. Rodrigues

Citations in the corpus

• Molecular Docking: Shifting Paradigms in Drug Discovery (2019, methodology): “Therefore, it represents an efficient tool to identify receptor conformations for docking [70,85] and to evaluate the stability of the predicted complexes [33,34].”
• Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development (2020, methodology): “Therefore, frequently after selecting one of the complexes (usually the highest-ranked complex), an MD simulation is conducted to explore the complex in much greater detail [50].”