From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output

Hanna Baltrukevich, Sabina Podlewska
2022 Frontiers in Pharmacology  
An increasing number of crystal structures available on one side, and the boost of computational power available for computer-aided drug design tasks on the other, have caused that the structure-based drug design tools are intensively used in the drug development pipelines. Docking and molecular dynamics simulations, key representatives of the structure-based approaches, provide detailed information about the potential interaction of a ligand with a target receptor. However, at the same time,
more » ... ey require a three-dimensional structure of a protein and a relatively high amount of computational resources. Nowadays, as both docking and molecular dynamics are much more extensively used, the amount of data output from these procedures is also growing. Therefore, there are also more and more approaches that facilitate the analysis and interpretation of the results of structure-based tools. In this review, we will comprehensively summarize approaches for handling molecular dynamics simulations output. It will cover both statistical and machine-learning-based tools, as well as various forms of depiction of molecular dynamics output.
doi:10.3389/fphar.2022.844293 pmid:35359865 pmcid:PMC8960308 fatcat:a5hw6tqawne3vg46scvjcxrg4u