PBxplore

PBxplore encodes local protein backbone conformation into a one-dimensional sequence of sixteen Protein Blocks (PBs) to analyze local structure and quantify protein flexibility and deformability.

Key Features:

• Protein Block encoding: Reduces three-dimensional local backbone structure to a one-dimensional sequence where each amino acid conformation is represented by one of sixteen distinct Protein Blocks.
• Local flexibility and deformability analysis: Analyzes local protein dynamics and deformability using the reduced PB conformational alphabet.
• Quantitative outputs: Generates frequencies, entropy, and information logos as outputs for conformational analysis.
• Molecular dynamics dataset processing: Processes large-scale molecular dynamics simulation datasets to extract PB-based conformational information.

Scientific Applications:

• Protein dynamics and deformability studies: Characterizes local conformational variability and flexibility in molecular biology and bioinformatics research.
• Analysis of molecular dynamics simulations: Extracts local conformational profiles from MD trajectories to study behavior beyond static structural snapshots.

Methodology:

Converts three-dimensional local backbone structure into a one-dimensional PB sequence with sixteen Protein Blocks per residue, processes molecular dynamics simulation datasets, and computes frequencies, entropy, and information logos presented as text files and graphical representations.