Application repository and science gateway for running molecular docking and dynamics simulations

Area of Science:

• Computational Biology
• Bioinformatics
• Environmental Science

Background:

• In silico tools like molecular docking and dynamics are crucial in various scientific fields.
• Current tools demand significant computational resources and technical expertise, limiting accessibility for many bio-scientists.
• There is a need for user-friendly platforms that democratize access to advanced computational modeling.

Purpose of the Study:

• To develop and demonstrate a science gateway solution for simplified in silico molecular modeling.
• To enable bio-scientists to perform complex computational studies without deep technical knowledge.
• To facilitate resource savings and broaden the scope of investigated molecular scenarios.

Main Methods:

• Development of a science gateway integrating Distributed Computing Infrastructures (clouds, grids).
• Definition and deconstruction of four molecular modeling scenarios to identify common building blocks.
• Implementation of a reference scenario on the EDGI infrastructure for pharmaceutical impact assessment.

Main Results:

• The science gateway successfully abstracts infrastructure complexities, allowing bio-scientists to execute modeling tasks.
• Identified common building blocks support the creation of diverse and complex use-cases.
• A reference implementation demonstrated the feasibility of assessing pharmaceutical impacts on aquatic indicator species.

Conclusions:

• The science gateway approach effectively democratizes in silico molecular modeling for bio-scientists.
• This solution enhances research efficiency, reduces resource demands, and expands investigative possibilities.
• The platform shows promise for addressing environmental concerns, such as pharmaceutical pollution in water bodies.