{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T16:39:10Z","timestamp":1775839150359,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005465","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T00:00:00Z","timestamp":1492992000000}}],"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2017,4,10]],"date-time":"2017-04-10T00:00:00Z","timestamp":1491782400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health (US)","doi-asserted-by":"crossref","award":["GM105991"],"award-info":[{"award-number":["GM105991"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005465","type":"journal-article","created":{"date-parts":[[2017,4,10]],"date-time":"2017-04-10T13:23:57Z","timestamp":1491830637000},"page":"e1005465","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":33,"title":["Amino acid composition predicts prion activity"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9129-1189","authenticated-orcid":true,"given":"Fayyaz ul Amir","family":"Afsar Minhas","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric D.","family":"Ross","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8269-6942","authenticated-orcid":true,"given":"Asa","family":"Ben-Hur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2017,4,10]]},"reference":[{"issue":"9","key":"ref1","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/ftv087","article-title":"A brief history of prions","volume":"73","author":"MD Zabel","year":"2015","journal-title":"Pathogens and Disease"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1186\/1743-422X-8-559","article-title":"An overview of human prion diseases","volume":"8","author":"M Imran","year":"2011","journal-title":"Virology Journal"},{"issue":"31","key":"ref3","doi-asserted-by":"publisher","first-page":"13010","DOI":"10.1073\/pnas.0903691106","article-title":"Inclusion formation and neuronal cell death through neuron-to-neuron transmission of alpha-synuclein","volume":"106","author":"P Desplats","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7","key":"ref4","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/ncb1901","article-title":"Transmission and spreading of tauopathy in transgenic mouse brain","volume":"11","author":"F Clavaguera","year":"2009","journal-title":"Nature Cell Biology"},{"issue":"27","key":"ref5","doi-asserted-by":"publisher","first-page":"11025","DOI":"10.1073\/pnas.1206555109","article-title":"Purified and synthetic Alzheimer\u2019s amyloid beta prions","volume":"109","author":"J St\u00f6hr","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"2","key":"ref6","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1111\/1574-6976.12053","article-title":"Physiological and environmental control of yeast prions","volume":"38","author":"TA Chernova","year":"2014","journal-title":"FEMS microbiology reviews"},{"issue":"1","key":"ref7","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.cell.2009.02.044","article-title":"A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins","volume":"137","author":"S Alberti","year":"2009","journal-title":"Cell"},{"issue":"4","key":"ref8","doi-asserted-by":"publisher","first-page":"311","DOI":"10.4161\/pri.18304","article-title":"The complexity and implications of yeast prion domains","volume":"5","author":"Z Du","year":"2011","journal-title":"Prion"},{"issue":"11","key":"ref9","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1038\/ncb1105-1039","article-title":"Prion domains: sequences, structures and interactions","volume":"7","author":"ED Ross","year":"2005","journal-title":"Nature Cell Biology"},{"issue":"36","key":"ref10","doi-asserted-by":"publisher","first-page":"12825","DOI":"10.1073\/pnas.0506136102","article-title":"Primary sequence independence for prion formation","volume":"102","author":"ED Ross","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1","key":"ref11","doi-asserted-by":"publisher","first-page":"e1004013","DOI":"10.1371\/journal.pcbi.1004013","article-title":"What Makes a Protein Sequence a Prion?","volume":"11","author":"R Sabate","year":"2015","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"ref12","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1080\/19336896.2015.1053685","article-title":"Amyloids or prions? That is the question","volume":"9","author":"R Sabate","year":"2015","journal-title":"Prion"},{"key":"ref13","first-page":"gkv490","article-title":"PrionW: a server to identify proteins containing glutamine\/asparagine rich prion-like domains and their amyloid cores","author":"R Zambrano","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"5158","key":"ref14","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1126\/science.7909170","article-title":"[URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae","volume":"264","author":"RB Wickner","year":"1994","journal-title":"Science"},{"issue":"5","key":"ref15","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1111\/j.1365-2958.1993.tb01159.x","article-title":"Deletion analysis of the SUP35 gene of the yeast Saccharomyces cerevisiae reveals two non-overlapping functional regions in the encoded protein","volume":"7","author":"MD Ter-Avanesyan","year":"1993","journal-title":"Molecular microbiology"},{"issue":"6","key":"ref16","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1128\/MCB.19.6.4516","article-title":"Two prion-inducing regions of Ure2p are nonoverlapping","volume":"19","author":"ML Maddelein","year":"1999","journal-title":"Molecular and Cellular Biology"},{"issue":"5233","key":"ref17","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1126\/science.270.5233.93","article-title":"Prion-inducing domain of yeast Ure2p and protease resistance of Ure2p in prion-containing cells","volume":"270","author":"DC Masison","year":"1995","journal-title":"Science"},{"issue":"22","key":"ref18","doi-asserted-by":"publisher","first-page":"11910","DOI":"10.1073\/pnas.97.22.11910","article-title":"A census of glutamine\/asparagine-rich regions: implications for their conserved function and the prediction of novel prions","volume":"97","author":"MD Michelitsch","year":"2000","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"6","key":"ref19","doi-asserted-by":"publisher","first-page":"R40","DOI":"10.1186\/gb-2003-4-6-r40","article-title":"A method to assess compositional bias in biological sequences and its application to prion-like glutamine\/asparagine-rich domains in eukaryotic proteomes","volume":"4","author":"PM Harrison","year":"2003","journal-title":"Genome Biol"},{"issue":"1","key":"ref20","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/S1097-2765(00)80412-8","article-title":"Rnq1: an epigenetic modifier of protein function in yeast","volume":"5","author":"N Sondheimer","year":"2000","journal-title":"Molecular cell"},{"issue":"2","key":"ref21","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/S0092-8674(00)81565-2","article-title":"Molecular basis of a yeast prion species barrier","volume":"100","author":"A Santoso","year":"2000","journal-title":"Cell"},{"issue":"1","key":"ref22","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1128\/MCB.01140-09","article-title":"Compositional Determinants of Prion Formation in Yeast","volume":"30","author":"JA Toombs","year":"2010","journal-title":"Molecular and Cellular Biology"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/978-1-62703-438-8_16","article-title":"A bioinformatics method for identifying Q\/N-rich prion-like domains in proteins","author":"ED Ross","year":"2013","journal-title":"Tandem Repeats in Genes, Proteins, and Disease: Methods and Protocols"},{"issue":"1","key":"ref24","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1186\/1471-2164-14-316","article-title":"Discovering putative prion sequences in complete proteomes using probabilistic representations of Q\/N-rich domains","volume":"14","author":"VE Angarica","year":"2013","journal-title":"BMC Genomics"},{"issue":"17","key":"ref25","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1093\/bioinformatics\/btu310","article-title":"PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition","volume":"30","author":"AK Lancaster","year":"2014","journal-title":"Bioinformatics"},{"key":"ref26","article-title":"The Rho termination factor of Clostridium botulinum contains a prion-like domain with a highly amyloidogenic core","volume":"6","author":"I Pallar\u00e8s","year":"2015","journal-title":"Frontiers in microbiology"},{"issue":"21","key":"ref27","doi-asserted-by":"publisher","first-page":"6065","DOI":"10.1073\/pnas.1604478113","article-title":"Luminidependens (LD) is an Arabidopsis protein with prion behavior","volume":"113","author":"S Chakrabortee","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"374","key":"ref28","article-title":"Drosophila GAGA factor polyglutamine domains exhibit prion-like behavior","volume":"14","author":"M Tariq","year":"2013","journal-title":"BMC genomics"},{"issue":"16","key":"ref29","doi-asserted-by":"publisher","first-page":"3435","DOI":"10.1093\/bioinformatics\/bti537","article-title":"FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded","volume":"21","author":"J Prilusky","year":"2005","journal-title":"Bioinformatics"},{"issue":"3","key":"ref30","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/nmeth.1432","article-title":"Exploring the sequence determinants of amyloid structure using position-specific scoring matrices","volume":"7","author":"S Maurer-Stroh","year":"2010","journal-title":"Nature Methods"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.artint.2013.06.003","article-title":"Multiple instance classification: Review, taxonomy and comparative study","volume":"201","author":"J Amores","year":"2013","journal-title":"Artificial Intelligence"},{"issue":"28","key":"ref32","doi-asserted-by":"publisher","first-page":"8584","DOI":"10.1073\/pnas.1501072112","article-title":"Generating new prions by targeted mutation or segment duplication","volume":"112","author":"KR Paul","year":"2015","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref33","first-page":"561","article-title":"Advances in Neural Information Processing Systems 15","author":"S Andrews","year":"2003"},{"issue":"18","key":"ref34","doi-asserted-by":"publisher","first-page":"i416","DOI":"10.1093\/bioinformatics\/bts416","article-title":"Multiple instance learning of Calmodulin binding sites","volume":"28","author":"FuAA Minhas","year":"2012","journal-title":"Bioinformatics"},{"issue":"10","key":"ref35","doi-asserted-by":"publisher","first-page":"e1000173","DOI":"10.1371\/journal.pcbi.1000173","article-title":"Support Vector Machines and Kernels for Computational Biology","volume":"4","author":"A Ben-Hur","year":"2008","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"ref36","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine learning"},{"issue":"1","key":"ref37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-48","article-title":"GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists","volume":"10","author":"E Eden","year":"2009","journal-title":"BMC bioinformatics"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.brainres.2012.01.016","article-title":"The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease","volume":"1462","author":"OD King","year":"2012","journal-title":"Brain research"},{"issue":"11","key":"ref39","doi-asserted-by":"publisher","first-page":"2047","DOI":"10.1007\/s00018-013-1543-6","article-title":"Yeast prions and human prion-like proteins: sequence features and prediction methods","volume":"71","author":"SM Cascarina","year":"2014","journal-title":"Cellular and Molecular Life Sciences"},{"key":"ref40","year":"2016","unstructured":"Pratt KM. Novel properties of hnRNP-UL1: its possible role in the pathogenesis of ALS. University of Birmingham; <year>2016<\/year>."},{"issue":"15","key":"ref41","doi-asserted-by":"publisher","first-page":"4103","DOI":"10.1093\/hmg\/ddu127","article-title":"A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G)","volume":"23","author":"NM Vieira","year":"2014","journal-title":"Human molecular genetics"},{"key":"ref42","unstructured":"Gitler AD. Gene targets associated with amyotrophic lateral sclerosis and methods of use thereof, US Patent 8,969,005; 2015."},{"issue":"21","key":"ref43","doi-asserted-by":"publisher","first-page":"7554","DOI":"10.1128\/MCB.23.21.7554-7565.2003","article-title":"Aggregation of expanded polyglutamine domain in yeast leads to defects in endocytosis","volume":"23","author":"AB Meriin","year":"2003","journal-title":"Molecular and Cellular Biology"},{"issue":"7043","key":"ref44","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1038\/nature03679","article-title":"Structural insights into a yeast prion illuminate nucleation and strain diversity","volume":"435","author":"R Krishnan","year":"2005","journal-title":"Nature"},{"issue":"5","key":"ref45","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1128\/MCB.01020-14","article-title":"Distinct amino acid compositional requirements for formation and maintenance of the [PSI+] prion in yeast","volume":"35","author":"KS MacLea","year":"2015","journal-title":"Molecular and cellular biology"},{"issue":"3","key":"ref46","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/nchembio.306","article-title":"Differences in prion strain conformations result from non-native interactions in a nucleus","volume":"6","author":"Y Ohhashi","year":"2010","journal-title":"Nature chemical biology"},{"issue":"10","key":"ref47","doi-asserted-by":"publisher","first-page":"e1003291","DOI":"10.1371\/journal.pcbi.1003291","article-title":"On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses","volume":"9","author":"PM Buck","year":"2013","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"ref48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1472-6807-7-1","article-title":"Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network","volume":"7","author":"A Malik","year":"2007","journal-title":"BMC Structural Biology"},{"issue":"11","key":"ref49","doi-asserted-by":"publisher","first-page":"4074","DOI":"10.1073\/pnas.0511295103","article-title":"The 3D profile method for identifying fibril-forming segments of proteins","volume":"103","author":"MJ Thompson","year":"2006","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"17","key":"ref50","doi-asserted-by":"publisher","first-page":"6519","DOI":"10.1073\/pnas.1119366109","article-title":"De novo design of synthetic prion domains","volume":"109","author":"JA Toombs","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1038\/srep34274","article-title":"Characterization of Amyloid Cores in Prion Domains","volume":"6","author":"R Sant\u2019Anna","year":"2016","journal-title":"Scientific Reports"},{"issue":"4","key":"ref52","doi-asserted-by":"publisher","first-page":"e86","DOI":"10.1371\/journal.pbio.0020086","article-title":"Dissection and design of yeast prions","volume":"2","author":"LZ Osherovich","year":"2004","journal-title":"PLoS Biol"},{"issue":"16","key":"ref53","doi-asserted-by":"publisher","first-page":"3436","DOI":"10.1128\/MCB.05338-11","article-title":"A small, glutamine-free domain propagates the [SWI+] prion in budding yeast","volume":"31","author":"ET Crow","year":"2011","journal-title":"Molecular and cellular biology"},{"issue":"7144","key":"ref54","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1038\/nature05848","article-title":"Prion recognition elements govern nucleation, strain specificity and species barriers","volume":"447","author":"PM Tessier","year":"2007","journal-title":"Nature"},{"issue":"7442","key":"ref55","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/nature11922","article-title":"Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS","volume":"495","author":"HJ Kim","year":"2013","journal-title":"Nature"},{"issue":"2","key":"ref56","doi-asserted-by":"publisher","first-page":"e31785","DOI":"10.1371\/journal.pone.0031785","article-title":"PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena","volume":"7","author":"D Harbi","year":"2012","journal-title":"PLoS ONE"},{"issue":"5","key":"ref57","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1093\/bioinformatics\/btq003","article-title":"CD-HIT Suite: a web server for clustering and comparing biological sequences","volume":"26","author":"Y Huang","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"ref58","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s10107-010-0420-4","article-title":"Pegasos: Primal estimated sub-gradient solver for SVM","volume":"127","author":"S Shalev-Shwartz","year":"2007","journal-title":"Mathematical Programming"},{"key":"ref59","first-page":"566","article-title":"The spectrum kernel: a string kernel for SVM protein classification","author":"C Leslie","year":"2002","journal-title":"The spectrum kernel: a string kernel for SVM protein classification"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005465","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T00:00:00Z","timestamp":1492992000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005465","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T17:12:23Z","timestamp":1540314743000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005465"}},"subtitle":[],"editor":[{"given":"Predrag","family":"Radivojac","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,4,10]]},"references-count":59,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,4,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005465","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1005465","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,4,10]]}}}