Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Area of Science:

• Computational biology
• Structural bioinformatics
• Bioinformatics tools

Background:

• Protein 3D structure analysis is crucial for understanding function.
• Comparing protein structures computationally is challenging.
• Existing methods may not efficiently handle large structural datasets.

Purpose of the Study:

• To develop a novel methodology for protein structure comparison and analysis.
• To encode protein 3D structures into 1D sequences using Protein Blocks (PBs).
• To create a user-friendly server (PBE) for these analyses.

Main Methods:

• Utilizing the 16 motifs of Protein Blocks (PBs) as a structural alphabet.
• Encoding protein structures into sequences of PBs.
• Applying dynamic programming with a substitution matrix for PB sequence alignment.
• Implementing the methodology in the Protein Block Expert (PBE) server.

Main Results:

• Developed a robust methodology for comparing protein structures via PB sequence alignment.
• Created the Protein Block Expert (PBE) server with tools for structure transformation (PBE-T), pairwise comparison (PBE-ALIGNc), and database mining (PBE-ALIGNm).
• Established a database (PBE-SAdb) of preprocessed PB sequences and alignments from the SCOP database.

Conclusions:

• The PBE server provides effective solutions for protein structure comparison and identification.
• Encoding protein structures using PBs offers a new avenue for structural analysis and discovery.
• The PBE server is freely accessible, promoting broader use in the research community.