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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
T Aleksiev1, R Potestio, F Pontiggia
1Scuola Internazionale Superiore di Studi Avanzati and eLab, CNR-INFM Democritos Simulation Centre, via Beirut 2-4, 34151 Trieste and Italian Institute of Technology, Genoa, Italy.
The PiSQRD web resource identifies quasi-rigid dynamical domains within protein structures. This tool aids in understanding protein dynamics by grouping amino acids that move as rigid units during fluctuations.
Area of Science:
- Structural biology
- Computational biophysics
Background:
- Protein dynamics are crucial for function.
- Identifying quasi-rigid domains aids in understanding these dynamics.
Purpose of the Study:
- To present the PiSQRD web resource for subdividing protein structures into quasi-rigid dynamical domains.
- To provide a tool for analyzing protein internal fluctuations.
Main Methods:
- Input: biomolecular structure and desired fluctuation fraction.
- Calculation of lowest energy fluctuation modes.
- Identification of rigid subunits based on domain motion.
Main Results:
- The PiSQRD server effectively subdivides protein structures into dynamical domains.
- Optimal subdivisions are identified based on user-defined fluctuation fractions.
- Results are presented via interactive graphics and detailed data output.
Conclusions:
- PiSQRD enables the subdivision of protein structures into quasi-rigid dynamical domains.
- This facilitates the analysis of protein equilibrium fluctuations and domain motion.
- The web resource offers an interactive and data-rich output for researchers.
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