title: Fibpredictor: a computational method for rapid prediction of amyloid fibril structures.
abstract: Amyloid 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 fibrils in atomistic detail are rare. To address this limitation, we have developed a novel, rapid computational method to predict amyloid fibril structures (Fibpredictor). The method combines β-sheet model building, β-sheet replication, and symmetry operations with side-chain prediction and statistical scoring functions. When applied to nine amyloid fibrils with experimentally determined structures, the method predicted the correct structures of amyloid fibrils and enriched those among the top-ranked structures. These models can be used as the initial heuristic structures for more complicated computational studies. Fibpredictor is available at http://nanohub.org/resources/fibpredictor .
authors: Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
authors: Hamed
authors: H
authors: Tabatabaei Ghomi
authors: Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN, USA.
authors: Elizabeth M
authors: EM
authors: Topp
authors: Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA. mlill@purdue.edu.
authors: Markus A
authors: MA
authors: Lill
mesh_terms: D000544:Alzheimer Disease; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D003198:Computer Simulation; D006801:Humans; D008956:Models, Chemical; D010300:Parkinson Disease; D010446:Peptide Fragments / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments
keywords: Amyloid fibrils; Statistical scoring functions; Structure prediction