ProMod3

ProMod3 performs homology modeling to generate protein structural models from sequence information, leveraging the OpenStructure framework for computational structural biology and protein structure prediction.

Key Features:

• Homology modeling: Generates protein models by exploiting sequence similarity to known structures.
• Template identification: Identifies suitable template structures among known proteins based on sequence similarity.
• Loop modeling: Implements loop modeling for reconstructing variable or missing regions in models.
• Sidechain modeling: Performs sidechain modeling to place amino-acid sidechains within modeled structures.
• Full-model generation: Constructs complete protein models by homology from target sequences and templates.
• Modular architecture: Provides a modular architecture for rapid prototyping and customization of modeling algorithms and pipelines.
• Production-ready pipelines: Includes production-ready pipelines for common homology modeling tasks.
• Scriptability: Is fully scriptable to enable automation and integration into larger computational workflows.
• OpenStructure integration: Leverages the OpenStructure framework as its computational infrastructure.
• SWISS-MODEL integration: Integrates with the SWISS-MODEL web server for deployment and use in established modeling services.

Scientific Applications:

• Protein structure prediction: Predicts tertiary structures of proteins from sequence using homology-based approaches.
• Complementing experimental data: Provides structural models to complement, interpret, and extend experimental structural data.
• Drug discovery: Supplies homology models of target proteins to support structure-based drug discovery efforts.
• Algorithm development: Enables development and prototyping of novel modeling algorithms and customized workflows.
• Modeling when experimental determination is limited: Allows generation of structural hypotheses for proteins lacking experimentally determined structures.

Methodology:

Identifies suitable template structures based on sequence similarity, performs loop modeling and sidechain modeling, and generates complete homology-derived protein models within a modular, scriptable framework implemented on OpenStructure.