Scop3D: three-dimensional visualization of sequence conservation.

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• Integrating protein structure and sequence variation is crucial for understanding protein evolution, function, and immunogenicity.
• Current methods for analyzing sequence conservation on protein structures are complex and not straightforward.

Purpose of the Study:

• To develop an automated tool, scop3D, for integrating protein sequence variation with 3D structure.
• To facilitate the analysis of protein sequence conservation and its mapping onto structural data.

Main Methods:

• Developed the Sequence Conservation on Protein 3D structure (scop3D) tool.
• Automated the process of creating multiple sequence alignments, calculating conservation, and mapping data onto protein structures.
• Modified PDB files to include sequence conservation or information entropy at each position.

Main Results:

• scop3D automatically generates modified PDB files with conservation data and provides associated text files with amino acid occurrences.
• The tool also generates spatial snapshots of the protein structure.
• Demonstrated utility in analyzing fusion proteins of respiratory syncytial virus and mumps virus.

Conclusions:

• scop3D simplifies the integration of sequence variation and protein structure data.
• The tool's visualizations can aid in vaccine development and identifying antigenic hotspots.