Foldit Standalone

Foldit Standalone provides an interactive interface to the Rosetta molecular modeling package for real-time manipulation, visualization, and computational refinement of protein structures.

Key Features:

• Rosetta integration: Interfaces directly with the Rosetta molecular modeling package to access Rosetta scoring, sampling, and modeling protocols.
• Electron density and contact map visualizations: Visualizes electron density and contact maps to aid interpretation and analysis of structural data.
• Multiple sequence alignment for template-based modeling: Provides multiple sequence alignment tools to support comparative and template-based modeling workflows.
• Rigid-body transformation controls: Enables manipulation of protein substructures for docking and conformational adjustments.
• RosettaScripts support and embedded Lua interpreter: Supports RosettaScripts and an embedded Lua interpreter for scripting and automation of modeling tasks.

Scientific Applications:

• Protein structure prediction: Uses Rosetta protocols and alignment tools to support prediction of protein tertiary structures.
• Protein design: Facilitates computational design and refinement of protein sequences and structures using Rosetta algorithms.
• Comparative/template-based modeling: Supports template-based model building through multiple sequence alignments and Rosetta refinement.
• Docking and conformational adjustment: Enables rigid-body manipulations relevant to docking and exploration of conformational space.
• Model interpretation and refinement with experimental data: Uses electron density and contact map visualizations to interpret and refine structural models against experimental constraints.

Methodology:

Interfaces with the Rosetta molecular modeling package; supports RosettaScripts and an embedded Lua interpreter; implements multiple sequence alignment for template-based modeling; provides electron density and contact map visualization and rigid-body transformation controls; implemented in C++ with a custom rendering and event engine.