Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen...

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Chemistry

Background:

• The Protein Data Bank (PDB) is a primary repository for macromolecular structure data.
• PDB files frequently contain structural imperfections, including missing atoms, side chains, and alternate rotamers.
• Manual correction of these PDB file errors requires specialized software and technical expertise.

Purpose of the Study:

• To develop an accessible web server for repairing and analyzing protein structures.
• To automate the process of fixing common errors in PDB files, such as missing atoms and side chains.
• To provide secondary structure assignment and Ramachandran plot analysis for corrected protein structures.

Main Methods:

• The Protein Repair and Analysis Server (PRAS) processes PDB files through distinct modules.
• Subroutines address sequence microheterogeneity, rotamers, missing atoms/side chains, and hydrogen atoms.
• Secondary structure elements are assigned based on backbone amide-amide interactions.

Main Results:

• PRAS successfully identifies and corrects various structural irregularities in PDB files.
• A detailed log file documents all detected issues and the implemented fixes.
• The server generates corrected PDB files, secondary structure assignments, and Ramachandran plots for download.

Conclusions:

• PRAS provides a user-friendly platform for repairing and analyzing protein structural data.
• The server supports both PDB and mmCIF formats, enhancing its utility.
• PRAS is freely available online and as downloadable source code for local installation.