PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet (Unknown language)

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Analyzing the data from molecular dynamics simulation of biological macromolecules like proteins is challenging. We propose a simple tool called PBmapclust that is based on a well established structural alphabet called Protein blocks (PB). PBs help in tracing the trajectory of the protein backbone by categorizing it into 16 distinct structural states. PBmapclust provides a time vs. amino acid residue plot that is color coded to match each of the PBs. Color changes correspond to structural changes, giving a visual overview of the simulation. Further, PBmapclust enables the user to "map" the conformational space sampled by the protein during the MD simulation by clustering the conformations. The ability to generate sub-maps for specific residues and specific time intervals allows the user to focus on residues of interest like for active sites or disordered regions. We have included an illustrative case study to demonstrate the utility of the tool. It describes the effect of the disordered domain of a HSP90 co-chaperone on the conformation of its active site residues. The scripts required to perform PBmapclust are made freely available under the GNU general public license.

Table of contents conference proceedings

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A Massively Parallel CUDA Algorithm to Compute and Visualize the Solvent Excluded Surface for Dynamic Molecular Data
Schäfer, Marco / Krone, Michael | 2019
QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces
Martinez, Xavier / Krone, Michael / Baaden, Marc | 2019
MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures
Skånberg, Robin / Linares, Mathieu / Falk, Martin / Hotz, Ingrid / Ynnerman, Anders | 2019
PBmapclust: Mapping and Clustering the Protein Conformational Space Using a Structural Alphabet
Vetrivel, Iyanar / Hoffmann, Lionel / Guegan, Sean / Offmann, Bernard / Laurent, Adele D. | 2019