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PDBFlex: exploring flexibility in protein structures.

Thomas Hrabe1, Zhanwen Li1, Mayya Sedova1

  • 1Bioinformatics and Systems Biology Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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|November 29, 2015
PubMed
Summary
This summary is machine-generated.

The PDBFlex database offers insights into protein structure flexibility by analyzing variations in deposited models from the Protein Data Bank (PDB). It provides tools to visualize and examine these structural differences for proteins with high sequence identity.

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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.