FeatureMap3D

FeatureMap3D maps protein sequence features and sequence conservation onto homologous Protein Data Bank (PDB) 3D structures to facilitate structural interpretation of annotations such as post-translational modifications, protease cleavage sites, and exonic boundaries.

Key Features:

• Annotation mapping: Maps user-provided sequence annotations including post-translational modifications, protease cleavage sites, and exonic structures onto homologous PDB structures.
• Homology search: Searches for homologous protein structures in the Protein Data Bank to identify target structures for mapping.
• Annotated sequence alignment: Produces sequence alignments annotated with user-defined features and conservation between query and target sequences.
• 3D structure visualization: Generates images of 3D protein structures with mapped annotations and sequence conservation coloring.
• Output formats: Exports results in parsable text format and as a PyMOL script file for structural visualization customization.
• Sequence conservation analysis: Colors 3D structures by sequence conservation to assess alignment quality between input sequences and homologous PDB structures.

Scientific Applications:

• Structural biology: Visualizing annotated features on 3D structures to interpret protein architecture and function.
• Protein engineering: Informing design and modification of proteins through mapped structural context of annotations.
• Evolutionary studies: Inferring evolutionary relationships and functional conservation by analyzing sequence conservation across homologous structures.

Methodology:

Performs homology searches against the PDB, aligns query sequences to target structures, maps sequence annotations onto 3D coordinates, colors structures by sequence conservation, and exports parsable text and PyMOL script outputs.