pdbFun: mass selection and fast comparison of annotated PDB residues

Area of Science:

• Bioinformatics
• Structural Biology
• Computational Biology

Background:

• Protein Data Bank (PDB) is a vast repository of protein structures.
• Analyzing protein structures at the residue level is crucial for understanding function.
• Existing tools may lack comprehensive residue-level annotation and flexible search capabilities.

Purpose of the Study:

• To introduce pdbFun, a web server for residue-level structural and functional analysis of proteins.
• To provide fast access to the PDB organized as a database of annotated residues.
• To enable users to select and compare residue subsets across multiple protein structures.

Main Methods:

• pdbFun organizes the PDB with residue-level annotations including solvent exposure, ligand binding, cavity location, secondary structure, residue type, sequence patterns, domain information, and catalytic activity.
• Users can define custom residue subsets by combining these features.
• These selections can be used as probes or targets in structure comparison searches against single structures, other selections, or entire datasets.

Main Results:

• pdbFun offers efficient retrieval and analysis of annotated protein residue data.
• The server facilitates complex queries, such as identifying solvent-exposed, hydrophilic residues not in alpha-helices involved in nucleotide binding.
• Search results are presented in both tabular and graphical formats, showing aligned structural matches.

Conclusions:

• pdbFun serves as a valuable resource for detailed structural and functional analysis of proteins at the residue level.
• The web server's ability to perform flexible residue subset selection and comparison enhances protein structure analysis and discovery.
• pdbFun provides a user-friendly interface for exploring the PDB with rich residue-specific annotations.