A computational method for rapid prediction of amyloid beta-fibril structures

By Hamed Tabatabaei Ghomi1, Markus A. Lill1

1. Purdue University

A computational method for rapid prediction of amyloid beta-fibril structures

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Version 1.1 - published on 11 Aug 2016

doi:10.4231/D3V40K117 cite this

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Abstract

Amyloid-like fibrils are important in diseases such as Alzheimer’s disease and Parkinson’s disease, and are also a common instability in peptide and protein drug products. Despite their importance, experimental structures of amyloid-like fibrils in atomistic detail are rare. To address this limitation, we have developed a novel, rapid computational method to predict amyloid-like fibril structures (Fibpredictor). The method combines b-sheet model building, b-sheet replication and symmetry operations with side-chain prediction and statistical scoring functions.

The method is fully described in Tabatabaei Ghomi, H., Topp, E.M. & Lill, M.A. Journal of  Molecular Modeling (2016) 22: 206. doi:10.1007/s00894-016-3066-1 . Please cite this reference if you use the tool.

References

Hamed Tabatabaei Ghomi., Elizabeth M. Topp, and Markus A. Lill, "Fibpredictor: A computational method for rapid prediction of amyloid β-fibril structures" Journal of  Molecular Modeling (2016) 22: 206. doi:10.1007/s00894-016-3066-1

Hamed Tabatabaei Ghomi, Jared J. Thompson, and Markus A. Lill. "Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?." Journal of bioinformatics and computational biology 12.05 (2014).

Cite this work

Researchers should cite this work as follows:

  • Hamed Tabatabaei Ghomi., Elizabeth M. Topp, and Markus A. Lill, "Fibpredictor: A computational method for rapid prediction of amyloid β-fibril structures" Journal of  Molecular Modeling (2016) 22: 206. doi:10.1007/s00894-016-3066-1

  • Hamed Tabatabaei Ghomi; Markus A. Lill (2016), "A computational method for rapid prediction of amyloid beta-fibril structures," http://nanohub.org/resources/fibpredictor. (DOI: 10.4231/D3V40K117).

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