The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and...

Area of Science:

• Computational biology
• Biophysics
• Virology

Background:

• Viruses are ubiquitous and pose significant threats to humans, animals, and plants.
• Rapid response to viral threats requires accurate assessment and effective countermeasures.
• In silico methods accelerate the understanding of virus activity and host interactions.

Purpose of the Study:

• To systematically review the application of the three-dimensional reference interaction site model (3D-RISM) for hydrated virus calculations since 2010.
• To summarize the biophysical insights gained from 3D-RISM studies.
• To evaluate the capabilities, limitations, achievements, and future prospects of 3D-RISM in virology.

Main Methods:

• Systematic literature review of 3D-RISM calculations for hydrated viruses.
• Analysis of biophysical aspects derived from 3D-RISM results.
• Case studies using influenza, hepatitis, and SARS-CoV-2 viruses.

Main Results:

• 3D-RISM enables efficient and detailed calculations of hydrated viruses, preserving molecular and liquid environment specifics.
• The method has been increasingly applied to study viruses like influenza, hepatitis, and SARS-CoV-2.
• 3D-RISM provides molecular insights into virus functioning and virus-host interactions.

Conclusions:

• 3D-RISM is a powerful, cost-effective computational tool for investigating hydrated viruses.
• The method offers significant potential for understanding viral mechanisms and informing countermeasure development.
• Continued application of 3D-RISM is expected to advance virological research, especially in response to pandemics.