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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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A general sequence processing and analysis program for protein engineering.

Ryan L Stafford1, Erik S Zimmerman, Trevor J Hallam

  • 1Protein Engineering, Sutro Biopharma, Inc. , 310 Utah Avenue Suite 150, South San Francisco, California 94080, United States.

Journal of Chemical Information and Modeling
|September 23, 2014
PubMed
Summary
This summary is machine-generated.

XLibraryDisplay is a free, open-source software for protein engineering that automates DNA sequence processing and activity correlation. This tool aids in efficient lead identification by analyzing DNA libraries and correlating sequence data with experimental results.

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Area of Science:

  • Biotechnology
  • Computational Biology
  • Molecular Biology

Background:

  • Protein engineering projects generate large DNA sequence datasets.
  • Existing software often lacks integrated sequence processing and activity correlation for lead identification.

Purpose of the Study:

  • To introduce XLibraryDisplay, an open-source software for automated DNA sequence processing and activity correlation.
  • To facilitate efficient lead identification in protein engineering.

Main Methods:

  • XLibraryDisplay integrates with Microsoft Excel for a user-friendly interface.
  • Automates batch processing of DNA sequences (raw, FASTA, Phred PHD formats).
  • Includes library composition analysis, data filtering, graphing, and structural alignment.

Main Results:

  • The software automates trimming, filtering, translation, and alignment of DNA sequences.
  • Enables correlation of sequence data with experimental results and structural data.
  • Generates PyMOL visualization scripts for structural analysis.

Conclusions:

  • XLibraryDisplay streamlines DNA sequence analysis for protein engineering lead discovery.
  • It is particularly effective for datasets of up to 10,000 characterized clones.
  • The software is freely available for download.