MODexplorer

MODexplorer explores sequence, structural, and functional diversity within protein families to support homology modeling and functional annotation transfer.

Key Features:

• Input Flexibility: Accepts either the amino acid sequence or the three-dimensional structure of a protein as input.
• Comprehensive Alignments: Generates alignments with homologous proteins that are annotated for downstream analysis.
• Rich Annotations: Provides sequence conservation, similarity scores, predicted secondary structure, predicted disorder regions, identification of ligand-, DNA-, and RNA-binding sites, and crystallographic resolution and quality scores for homologous structures.
• Comparative Analysis: Enables analysis of sequence and structural conservation to identify differing conformational states or ligand interactions among homologs.
• Template Selection for Modeling: Assists selection of appropriate templates for comparative modeling by considering available annotations and homologous-structure data.

Scientific Applications:

• Homology Modeling: Supports selection of templates and annotation-informed construction of comparative structural models.
• Functional Annotation Transfer: Facilitates prediction of functional sites by transferring annotations from homologous proteins.
• Structural Biology Research: Provides annotated alignments and structural data to study structure–function relationships and evolutionary conservation within protein families.

Methodology:

Generates alignments with homologous proteins and annotates them with sequence conservation, similarity scores, predicted secondary structure, predicted disorder regions, and predicted ligand/DNA/RNA binding sites; retrieves crystallographic resolution and quality scores for homolog structures; uses these annotations to inform template selection for comparative modeling.