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PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information

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Multiple Sequence Alignment Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1079))

Abstract

Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile–profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

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Acknowledgments

The work is supported in part by the National Institutes of Health (GM094575 to NVG) and the Welch Foundation (I-1505 to NVG).

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Jimin Pei

  2. Department of Biophysics, Howard Hughes Medical Institute, Dallas, TX, USA

    Nick V. Grishin

  3. Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Nick V. Grishin

Authors
  1. Jimin Pei
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  2. Nick V. Grishin
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Editor information

Editors and Affiliations

  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

    David J Russell

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Pei, J., Grishin, N.V. (2014). PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7_17

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  • DOI: https://doi.org/10.1007/978-1-62703-646-7_17

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-645-0

  • Online ISBN: 978-1-62703-646-7

  • eBook Packages: Springer Protocols

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