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CX, DPX, and PCW: Web Servers for the Visualization of Interior and Protruding Regions of Protein Structures in 3D and 1D

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Prediction of Protein Secondary Structure

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1484))

Abstract

The CX and DPX web-based servers at http://pongor.itk.ppke.hu/bioinfoservices are dedicated to the analysis of protein 3D structures submitted by the users as Protein Data Bank (PDB) files. CX computes an atomic protrusion index, cx that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index, dpx for buried atoms, and allows one to visualize the distribution of buried residues. CX and DPX visualize 3D structures colored according to the calculated indices and return PDB files that can be visualized using standard programs. A combined server site, the Protein Core Workbench allows visualization of dpx, cx, solvent-accessible area as well as the number of atomic contacts as 3D plots and 1D sequence plots. Online visualization of the 3D structures and 1D sequence plots are available in all three servers. Mirror sites are available at http://hydra.icgeb.trieste.it/protein/.

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Author information

Authors and Affiliations

  1. Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u 50/a, Budapest, 1083, Hungary

    Balázs Ligeti, Roberto Vera, János Juhász & Sándor Pongor

  2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD, 20894, USA

    Roberto Vera

Authors
  1. Balázs Ligeti
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  2. Roberto Vera
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  3. János Juhász
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  4. Sándor Pongor
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Corresponding author

Correspondence to Sándor Pongor .

Editor information

Editors and Affiliations

  1. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yaoqi Zhou

  2. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA

    Andrzej Kloczkowski

  3. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA

    Eshel Faraggi

  4. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yuedong Yang

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Ligeti, B., Vera, R., Juhász, J., Pongor, S. (2017). CX, DPX, and PCW: Web Servers for the Visualization of Interior and Protruding Regions of Protein Structures in 3D and 1D. In: Zhou, Y., Kloczkowski, A., Faraggi, E., Yang, Y. (eds) Prediction of Protein Secondary Structure. Methods in Molecular Biology, vol 1484. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6406-2_20

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  • DOI: https://doi.org/10.1007/978-1-4939-6406-2_20

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6404-8

  • Online ISBN: 978-1-4939-6406-2

  • eBook Packages: Springer Protocols

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