bioRxiv2018
AmyCo: the Amyloidoses CollectionAmyloid fibrils are formed when soluble proteins misfold into highly ordered insoluble fibrillar aggregates and affect various organs and tissues. The deposition of amyloid fibrils is the main hallmark of a group of disorders, called amyloidoses. Curiously, fibril deposition has been also recorded as a complication in a number of other pathological conditions, including well-known neurodegenerative or endocrine diseases. To date, amyloidoses are roughly classified, owing to their tremendous heterogeneity. In this work, we introduce AmyCo, a freely available collection of amyloidoses and clinical disorders related to amyloid deposition. AmyCo classifies 74 diseases associated with amyloid deposition into two distinct categories, namely 1) amyloidosis and 2) clinical conditions associated with amyloidosis. Each database entry is annotated with the major protein component (causative protein), other components of amyloid deposits and affected tissues or organs. Database entries are also supplemented with appropriate detailed annotation and are referenced to ICD-10, MeSH, OMIM, PubMed, AmyPro and UniProtKB databases. To our knowledge, AmyCo is the largest repository containing information about amyloidoses and diseases related to amyloid deposition. The AmyCo web interface is available at http://bioinformatics.biol.uoa.gr/amyco.\n\nKaterina C. Nastou is a Ph.D. student in Bioinformatics, at the Department of Biology of the National and Kapodistrian University of Athens. She is currently working on computational analysis of membrane and amyloidogenic proteins as part of her Ph.D. thesis. Her research focuses on the study of protein-protein interactions and the visualization and analysis of biological networks for these protein families, on the computational prediction of protein structure and function and the design and development of biological databases.\n\nGeorgia I. Nasi is a Ph.D. student in Biophysics, at the Department of Biology of the National and Kapodistrian University of Athens and a second year student in the Bioinformatics Masters Program, at the same department. She is currently conducting her Masters thesis on the computational analysis and visualization of the interaction network of amyloidoses and proteins associated with these disorders. Her research for her Ph.D. focuses on biophysical and computational analysis of amyloidogenic proteins and peptide-analogues associated with amyloidoses.\n\nDr. Paraskevi L. Tsiolaki is a Biologist with an MSc in Bioinformatics and a PhD in Molecular Biophysics. She is currently working as a postdoctoral fellow in Dr V. Iconomidous group, Assist. Prof. at the National and Kapodistrian University of Athens and her research interests focus on Molecular Biophysics and Structural Biology. Her current research efforts have been directed towards identifying the structural characteristics that underlie the self-assembly mechanisms,governing amyloidogenicity. More specifically she works on the structure and self-assembly of different amyloidogenic proteins or amyloidogenic peptide-analogues, implicated with amyloidoses, utilizing biophysical and biochemical techniques. She is also working on the computational and structural analysis of the anomalous type of protein-protein interactions in protein aggregation, with particular focus on the development of novel therapeutic intervention strategies.\n\nDr.Zoi Litou works as a Special Laboratory Teaching Staff in \"Bioinformatics-Biophysics\" at the Section of Cell Biology and Biophysics, Department of Biology, National &Kapodistrian University of Athens. She has a PhD in Bioinformatics. She is currently working on computational analysis of membrane proteins focusing on the automated recognition and classification of single-spanning membrane proteins, CWPs, GPCRs and Ion channels. Biological Network Analysis, Prediction algorithms, Algorithm Visualization techniques in Bioinformatics, High throughput sequencing analysis and visualization, Clustering Analysis, Knowledge discovery, management and representation, Data integration, Chemoinformatics, Pharmacogenomics, Text Mining in Bioinformatics, Personalized Medicine, Parallel programming.\n\nDr. Vassiliki A. Iconomidou is an Assistant Professor of Structural Biology/Molecular Biophysics and a group leader of Biophysics and Bioinformatics Lab at the Department of Biology of the National and Kapodistrian University of Athens. Her research interests include: 1) Structural and self-assembly studies of fibrous proteins, which form extracellular, proteinaceous structures of physiological importance like lepidopteran, dipteran and fish chorions and arthropod cuticle, 2) Structural and self-assembly studies of silkmoth chorion peptide-analogues as novel self-assembled polymers with amyloid properties, aiming at the construction of novel biomaterials with extraordinary physical properties, 3) Experimental studiesof the role of a great variety of amyloidogenic ( aggregation-prone) peptides, predicted by our AMYLPRED prediction algorithm, in several widespread and also rare pathological amyloidoses. She had been visiting European Molecular Biology Laboratory (EMBL Heidelberg) for more than ten years, conducting research on molecular self-assembly focusing especially on functional, protective and pathological amyloids and amyloidoses, and she was there when she published the first article on natural protective amyloids. She is the author of 41 publications and 6 book chapters which focus mostly on functional and pathological amyloid studies.