PyProtModel

PyProtModel facilitates comparative (homology) modeling of protein three-dimensional structures using MODELLER within a Python framework to generate and prepare PDB-format models for structural bioinformatics analyses.

Key Features:

• Integration with MODELLER: Direct use of MODELLER for template-based comparative modeling of protein structures.
• Automated homology modeling: Automation of modeling steps from sequence input to 3D structure prediction using template-based approaches.
• Configurable MODELLER options: Exposure of multiple MODELLER parameters and options to adapt modeling protocols to specific cases.
• Preparation and evaluation of PDB files: Functions for preparing and evaluating Protein Data Bank (PDB) files for downstream structural analyses.

Scientific Applications:

• Structural annotation: Generation of 3D models to support functional inference and structural annotation of protein sequences.
• Drug design and disease research: Provision of modeled protein structures to aid structure-based drug design and studies of molecular mechanisms in disease.
• Complementing experimental coverage: Computational expansion of structural coverage given that X-ray crystallography and other experimental methods have elucidated a small fraction of known protein sequences (less than one-thousandth).

Methodology:

Template-based (comparative/homology) modeling leveraging known structures via MODELLER with automated model-building steps and PDB preparation/evaluation.