Introduction

Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function determination is exceptionally time-consuming and can't keep pace with the identification of protein sequences. A tool, DASP (Deacon Active Site Profiler), was previously developed to identify protein sequences with active site similarity to a query set. Development of two iterative, automatable methods for clustering proteins into functionally relevant groups exposed algorithmic limitations to DASP.The accuracy and efficiency of DASP was significantly improved through six algorithmic enhancements implemented in two stages: DASP2 and DASP3. Validation demonstrated DASP3 provides greater score separation between true positives and false positives than earlier versions. In addition, DASP3 shows similar performance to previous versions in clustering protein structures into isofunctional groups (validated against manual curation), but DASP3 gathers and clusters protein sequences into isofunctional groups more efficiently than DASP and DASP2.DASP algorithmic enhancements resulted in improved efficiency and accuracy of identifying proteins that contain active site features similar to those of the query set. These enhancements provide incremental improvement in structure database searches and initial sequence database searches; however, the enhancements show significant improvement in iterative sequence searches, suggesting DASP3 is an appropriate tool for the iterative processes required for clustering proteins into isofunctional groups.

Publications

  1. DASP3: identification of protein sequences belonging to functionally relevant groups.
    Cite this
    Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS, 2016-11-01 - BMC bioinformatics

Credits

  1. Janelle B Leuthaeuser
    Developer

    Present address: University of Richmond, Gottwald Hall C302

  2. John H Morris
    Developer

    Department of Pharmaceutical Chemistry, University of California San Francisco, United States of America

  3. Angela F Harper
    Developer

    Department of Physics, Wake Forest University, United States of America

  4. Thomas E Ferrin
    Developer

    Department of Pharmaceutical Chemistry, University of California San Francisco, United States of America

  5. Patricia C Babbitt
    Developer

    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, United States of America

  6. Jacquelyn S Fetrow
    Investigator

    Department of Chemistry, University of Richmond, United States of America

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Summary
AccessionBT006770
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJacquelyn S Fetrow