PUDGE

PUDGE performs protein structure prediction for homology modeling by integrating multiple data sources and specialized modeling tools.

Key Features:

• Template selection: Selects templates based on sequence similarity and structural relevance.
• Alignment: Aligns the target sequence to selected templates to establish residue-level correspondences.
• Model building: Constructs preliminary structural models from aligned sequences using modeling tools.
• Model refinement: Refines structural details to improve accuracy and to reflect functional information.
• Model evaluation: Assesses models using analytical tools and comparative analyses to inform model selection.
• Stage-wise analysis: Provides visualization, analysis, and comparison of results at each modeling stage.
• Functional data integration: Incorporates functional information into modeling to address limitations of traditional approaches.

Scientific Applications:

• Homology modeling: Supports building protein structural models from homologous templates using sequence and structural information.
• Structure-based functional inference: Integrates functional data into structural models to interpret functional sites and consequences.
• Model assessment and selection: Enables evaluation and comparison of candidate models to select the most appropriate structure.

Methodology:

Modeling proceeds through five stages: template selection based on sequence similarity and structural relevance; sequence-to-template alignment; construction of preliminary models from aligned sequences; structural refinement to adjust details and incorporate functional information; and model evaluation using analytical comparisons.