PDBFlex: exploring flexibility in protein structures

Area of Science:

• Structural biology
• Bioinformatics
• Computational biology

Background:

• Protein Data Bank (PDB) contains multiple structural models for the same protein.
• Variations between these models reflect protein flexibility and dynamics.
• Analyzing these variations is crucial for understanding protein function.

Purpose of the Study:

• To introduce the PDBFlex database, a resource for protein structure flexibility.
• To provide tools for analyzing and visualizing structural variations within proteins.
• To facilitate the study of protein conformational changes.

Main Methods:

• Collected protein structures from PDB with >= 95% sequence identity.
• Analyzed structural differences between deposited models.
• Clustered structures based on similarity.
• Developed visualization tools including 2D-scaling of RMSD, local RMSD graphs, secondary structure difference plots, and 3D conformational transitions.

Main Results:

• PDBFlex database established, containing flexibility information from PDB depositions.
• Tools enable visualization of Root Mean Square Deviation (RMSD) distances and local structural variations.
• Analysis of secondary structure differences and unresolved residues is supported.
• 3D visualization of conformational changes is available via JSmol.

Conclusions:

• PDBFlex provides a valuable resource for exploring protein structural flexibility.
• The database and its tools facilitate in-depth analysis of protein conformational variability.
• This resource aids researchers in understanding protein dynamics and function.