Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

Area of Science:

• Computational Biology
• Biophysics
• Structural Bioinformatics

Background:

• The Rosetta software package offers extensive tools for biopolymer modeling and design.
• Current accessibility is limited by the need for Unix command-line expertise.
• The Rosetta Online Server that Includes Everyone (ROSIE) was developed to broaden access.

Purpose of the Study:

• To simplify the protocol specification format for the ROSIE web server.
• To increase the number and variety of Rosetta protocols available through ROSIE.
• To enhance accessibility of advanced biopolymer modeling tools for academic researchers.

Main Methods:

• Developed a new, single-file format for specifying Rosetta protocols.
• Integrated existing and new Rosetta applications into the simplified ROSIE framework.
• Expanded the ROSIE server with a wider range of computational biology protocols.

Main Results:

• The simplified protocol format has more than doubled the number of available Rosetta protocols on ROSIE.
• New applications include pKa determination, lipid accessibility, RNA redesign, and various docking strategies.
• The enhanced ROSIE server now supports protein-protein, protein-small molecule, and antibody docking, among others.

Conclusions:

• The simplified ROSIE protocol specification significantly enhances the usability and scope of the web server.
• ROSIE provides a more accessible platform for academic researchers to utilize advanced Rosetta modeling tools.
• The expansion of ROSIE protocols facilitates broader research in protein and nucleic acid design and analysis.