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A Protocol for Computer-Based Protein Structure and Function Prediction
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AMASS: a database for investigating protein structures.

Clinton J Mielke1, Lawrence J Mandarino2, Valentin Dinu2

  • 1Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USABiodesign Institute, Arizona State University, Tempe, AZ 85287, USA, The Center for Metabolic and Vascular Biology, Mayo Clinic, Scottsdale, AZ 85259, USA and Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA.

Bioinformatics (Oxford, England)
|February 6, 2014
PubMed
Summary
This summary is machine-generated.

The AMASS database integrates protein sequence annotations with 3D structures, aiding the study of functional residues and their co-localization. It analyzes mass spectrometry data for post-translational modifications in key protein locations.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Proteomics

Background:

  • Protein sequence annotation databases and structure portals exist but lack integrated exploration of functional residues.
  • Understanding functional residue co-localization is crucial for deciphering protein function.

Purpose of the Study:

  • To develop an integrated platform for exploring protein functional residues and their co-localization.
  • To enable analysis of mass spectrometry data for post-translational modifications in functionally relevant protein structural contexts.

Main Methods:

  • Developed the AMASS database, mapping 1D sequence annotations to 3D protein structures.
  • Implemented an intuitive visualization interface for exploring protein data.
  • Created an analysis service for screening mass spectrometry data.

Main Results:

  • The AMASS database provides integrated visualization of sequence and structure data.
  • The platform facilitates the identification of co-localized functional residues, including post-translational modifications.
  • Analysis service screens for post-translational modifications in functionally relevant structural locations.

Conclusions:

  • AMASS enhances the exploration of protein functional residues and their structural context.
  • The database aids in understanding the functional significance of co-localized residues and post-translational modifications.
  • AMASS serves as a valuable resource for researchers in bioinformatics, structural biology, and proteomics.