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Updated: May 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Seq2Ref: a web server to facilitate functional interpretation.

Wenlin Li1, Qian Cong, Lisa N Kinch

  • 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

BMC Bioinformatics
|January 30, 2013
PubMed
Summary
This summary is machine-generated.

Seq2Ref identifies experimentally validated reference proteins to improve the functional annotation of uncharacterized proteins. This approach enhances reliability over error-prone computational methods for protein sequence databases.

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Last Updated: May 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein sequence databases are rapidly expanding due to genome sequencing.
  • Most sequences lack experimental characterization, relying on potentially erroneous computational annotations.
  • Functional interpretation requires reliable annotations from experimentally validated or manually curated 'reference proteins'.

Purpose of the Study:

  • To develop a reliable method for identifying functionally relevant reference proteins for uncharacterized sequences.
  • To improve the accuracy of protein functional annotation in large sequence databases.

Main Methods:

  • The Seq2Ref server employs BLAST to find homologous proteins to a query sequence.
  • It identifies and ranks relevant reference proteins based on experimental characterization.
  • A plurality-based rating system evaluates homology and relevance.

Main Results:

  • Seq2Ref successfully identifies homologous proteins and associated reference proteins.
  • The server provides relevant publications detailing experimental characterizations.
  • A novel rating system ranks reference proteins by relevance to the query sequence.

Conclusions:

  • Seq2Ref offers insights into proteins of unknown function by linking them to characterized reference proteins.
  • This tool aids in developing a deeper understanding of uncharacterized proteins.
  • The Seq2Ref server is publicly accessible for use in protein research.