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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Automated protein structure calculation from NMR data.

Mike P Williamson1, C Jeremy Craven

  • 1Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. m.williamson@sheffield.ac.uk

Journal of Biomolecular NMR
|January 13, 2009
PubMed
Summary
This summary is machine-generated.

Automated protein structure determination software is nearing completion for small proteins (<15 kDa), enhancing objectivity and freeing up researchers. Key challenges remain in peak picking, shared calculation frameworks, and sample preparation for larger proteins.

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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology
  • Molecular Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique for determining protein structures.
  • Current computational methods require significant user intervention, limiting throughput and objectivity.
  • The goal of fully automated structure determination aims to streamline the process and improve reproducibility.

Purpose of the Study:

  • To assess the current state of automated protein structure determination using NMR data.
  • To identify key technological barriers hindering further automation.
  • To guide future development efforts, particularly for structural genomics initiatives.

Main Methods:

  • Review of current software capabilities for automated structure calculation from NMR spectra.
  • Analysis of the stages involved in protein structure determination, from spectral processing to validation.
  • Identification and categorization of technological bottlenecks in the automated workflow.

Main Results:

  • Software is nearing full automation for proteins under 15 kDa, enabling objective and validated structure calculations.
  • Automation can be extended to approximately 20 kDa with further development.
  • Major barriers include peak picking algorithms, a standardized framework for structure calculation and validation, and sample preparation for larger proteins.

Conclusions:

  • Fully automated protein structure determination is achievable for small proteins, enhancing research objectivity and efficiency.
  • Overcoming technological barriers in peak picking, computational frameworks, and sample preparation is crucial for advancing automation.
  • Focusing development on these barriers will benefit structural genomics consortia and the broader field of protein structure determination.