MaxMod

MaxMod performs protein homology modeling to construct accurate three-dimensional protein structures for structural and functional analysis.

Key Features:

• MODELLER integration: Uses the MODELLER program as the modeling engine to generate homology-based 3D protein models.
• Profile HMM integration: Employs profile Hidden Markov Models (HMMs) in conjunction with Clustal Omega to improve homologous template selection and target–template alignments.
• Template flexibility: Supports modeling with templates that contain modified residues to accommodate diverse protein chemistries.
• Loop optimization: Provides loop refinement procedures to improve conformations in variable or poorly conserved regions.
• Express modeling: Generates a protein model directly from an input sequence without additional alignment intervention.
• Automatic PDB updates: Updates the Protein Data Bank (PDB) database automatically to incorporate current structural templates.

Scientific Applications:

• Protein structure prediction: Produces homology models for use in structural characterization and hypothesis generation.
• Drug discovery: Supplies 3D models for structure-based ligand design and docking studies.
• Enzyme design: Provides structural models to support engineering of catalytic sites and substrate interactions.
• Protein function analysis: Facilitates investigation of molecular mechanisms and structure–function relationships.

Methodology:

Integrates the MODELLER program with profile HMMs and Clustal Omega to refine template selection and target–template alignments.