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MAPAS: a tool for predicting membrane-contacting protein surfaces

Nature Methods volume 5, page 119 (2008)Cite this article

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To the editor:

Many important biological processes, from serum phospholipid metabolism to amyloid disease, involve formation of protein-membrane complexes. Thus, tools for identifying membrane-contacting features in a protein structure are very important. However, few algorithmic approaches for membrane-contacting surface prediction have yet been reported1,2.

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Figure 1: The MAPAS algorithm workflow and performance.

References

  1. Lomise, A., Pogozheva, I., Lomize, M. & Mosberg, H. Protein Sci. 15, 1318–1333 (2006).

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  2. Scott, D., Diez, G. & Goldmann, W. Theor. Biol. Med. Model. 3, 17–20 (2006).

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Acknowledgements

Supported by US National Institutes of Health (AG18440 to I.F.T. and E.M., AI057695 for V.K. and S.K.N.) and Department of Energy (INCITE grant). We are grateful for computational support on IBM BlueGene computers at the San Diego Supercomputer Center and at the Argonne National Laboratory.

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Authors and Affiliations

  1. San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Yuriy Sharikov, Ross C Walker, Jerry Greenberg, Mark A Miller & Igor F Tsigelny

  2. Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Valentina Kouznetsova & Sanjay K Nigam

  3. Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Sanjay K Nigam

  4. Department of Neuroscience, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Eliezer Masliah

  5. Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Eliezer Masliah

  6. Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Igor F Tsigelny

Authors
  1. Yuriy Sharikov
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  2. Ross C Walker
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  3. Jerry Greenberg
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  4. Valentina Kouznetsova
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  5. Sanjay K Nigam
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  6. Mark A Miller
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  7. Eliezer Masliah
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  8. Igor F Tsigelny
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Corresponding author

Correspondence to Igor F Tsigelny.

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Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Table 1–3, Supplementary Methods, Supplementary Discussion (PDF 1446 kb)

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Sharikov, Y., Walker, R., Greenberg, J. et al. MAPAS: a tool for predicting membrane-contacting protein surfaces. Nat Methods 5, 119 (2008). https://doi.org/10.1038/nmeth0208-119

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