Bio3D-Web

Bio3D-Web provides interactive analysis of sequence-structure-dynamics relationships across user-defined protein structure sets to characterize structural, conformational, and dynamic properties of homologous proteins with high-resolution structures.

Key Features:

• Structure Database Searching: Search and select relevant protein structures from a structure database for downstream analysis.
• Sequence and Structure Conservation Assessment: Evaluate sequence and structural conservation across protein families to inform evolutionary and functional relationships.
• Inter-Conformer Relationship Mapping and Clustering: Map and cluster conformations using principal component analysis (PCA) to characterize conformational heterogeneity.
• Flexibility Prediction and eNMA Comparison: Predict structural flexibility and compare ensembles using ensemble normal mode analysis (eNMA) to quantify dynamic behavior.
• Custom Report Generation: Export analysis results and settings into PDF, Word, and HTML report formats.

Scientific Applications:

• Structural Biology: Characterize structural and conformational properties of protein families with available high-resolution structures.
• Molecular Dynamics and Dynamics Comparison: Quantitatively compare flexibility and motion across conformers and ensembles using eNMA and PCA-derived metrics.
• Evolutionary Studies: Assess sequence and structural conservation to investigate evolutionary relationships and functional implications.

Methodology:

Computational methods explicitly include structure database searching, sequence and structure conservation assessment, principal component analysis (PCA) for inter-conformer mapping and clustering, and ensemble normal mode analysis (eNMA) for flexibility prediction and comparison.