DisProt 7.0 : a major update of the database of disordered proteins

Published online 24 No embe 2016 Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue D219–D227 doi: 10.1093/na /gkw1056 DisP o 7.0: a majo upda e o he da abase o diso de ed p o eins Damiano Pio esan1,†, F ancesco Taba o1,2,†,I anMiˇ ce i´ c1, Ma co Necci1, Fede ica Quaglia1, Ch is ophe J. Old ield3, Ma ia C is ina Asp omon e4, No man E. Da ey5,6, Radosla Da ido i´ c7, Zsuzsanna Dosz ´ anyi8,9, A ne Elo sson10, Alessand a Gaspa ini4, And ´ as Ha os1,9, And ey V. Kaja a11,12,13, Lajos Kalma 9,14, Emanuela Leona di4, Tamas Laza 15,16, Sand a Macedo-Ribei o17, Mau icio Macossay-Cas illo15,16, A ila Mesza os9, Gio anni Mine ini1, Nikole a Mu ai9, Jo di Pujols18, Daniel B. Roche11,12, Edoa do Salladini19, E a Schad9, An oine Sch amm19, Bea a Szabo9, Agnes Tan os9, Fio ella Tonello1,20, Kons an inos D. Tsi igos10, Ne ena Veljko i´ c7, Sal ado Ven u a18, Wim V anken15,16,21, Pe Wa holm10, Vladimi N. U e sky22,23, A. Kei h Dunke 3, Sonia Longhi19,*, Pe e Tompa9,15,16,* and Sil io C.E. Tosa o1,20,* 1Depa men o Biomedical Sciences, Uni e si y o Pado a, I-35121 Pado a, I aly, 2Ins i u e o Biosciences and Medical Technology, Uni e si y o Tampe e, Finland, 3Cen e o Compu a ional Biology and Bioin o ma ics, Indiana Uni e si y School o Medicine, 46202 Indianapolis, IN, USA, 4Depa men o Woman and Child Heal h, Uni e si y o Pado a, I-35128 Pado a, I aly, 5Conway Ins i u e o Biomolecula & Biomedical Resea ch, Uni e si y College Dublin, Bel ield, Dublin 4, I eland, 6I eland UCD School o Medicine & Medical Science, Uni e si y College Dublin, Bel ield, Dublin 4, I eland, 7Cen e o Mul idisciplina y Resea ch, Ins i u e o Nuclea Sciences Vinca, Uni e si y o Belg ade, 11001 Belg ade, Se bia, 8MTA-ELTE Lend¨ ule Bioin o ma ics Resea ch G oup, Depa men o Biochemis y, E¨ o ¨ os Lo ´ and Uni e si y, 1/cP ´ azm´ any P´ e e s´ e ´ any, 1117 Budapes , Hunga y, 9Ins i u e o Enzymology, Resea ch Cen e o Na u al Sciences, Hunga ian Academy o Sciences, PO Box 7,H-1518 Budapes , Hunga y, 10Depa men o Biochemis y and Biophysics and Science o Li e Labo a o y, S ockholm Uni e si y, Box 1031, 17121 Solna, Sweden, 11Cen e de Reche che en Biologie cellulai e de Mon pellie (CRBM), UMR 5237 CNRS, Uni e si ´ e Mon pellie 1919 Rou e de Mende, Cedex 5, Mon pellie 34293, F ance, 12Ins i u de Biologie Compu a ionnelle (IBC), Mon pellie 34095, F ance, 13Uni e si y ITMO, Ins i u e o Bioenginee ing, S . Pe e sbu g 197101, Russia, 14Depa men o Ve e ina y Medicine, Uni e si y o Camb idge, Madingley Road, Camb idge CB3 0ES, UK, 15S uc u al Biology B ussels, V ije Uni e si ei B ussel (VUB), B ussels 1050, Belgium, 16S uc u al Biology Resea ch Cen e (SBRC), Flande s Ins i u e o Bio echnology (VIB), B ussels 1050, Belgium, 17Biomolecula S uc u e and Func ion G oup, Ins i u o de Biologia Molecula e Celula (IBMC) and Ins i u o de In es igac¸˜ ao e Ino ac¸˜ ao em Sa´ ude (i3S), Uni e sidade do Po o, 4200-135 Po o, Po ugal, 18Depa amen de Bioquimica i Biologia Molecula and Ins i u de Bio ecnologia i Biomedicina, Uni e si a Au ` onoma de Ba celona, Bella e a 08193, Spain, 19Aix-Ma seille Uni , CNRS, AFMB, UMR 7257, Ma seille, F ance, 20CNR Ins i u e o Neu osceince, I-35121 Pado a, I aly, 21In e uni e si y Ins i u e o Bioin o ma ics in B ussels (IB2), ULB-VUB, B ussels 1050, Belgium, 22Labo a o y o S uc u al Dynamics, S abili y and Folding o P o eins, Ins i u e o Cy ology, Russian Academy o Sciences, 194064 S . Pe e sbu g, Russia and 23Depa men o Molecula Medicine and USF Heal h By d Alzheime ’s Resea ch Ins i u e, Mo sani College o Medicine, Uni e si y o Sou h Flo ida, Tampa, FL 33612, USA Recei ed Sep embe 27, 2016; Re ised Oc obe 19, 2016; Edi o ial Decision Oc obe 20, 2016; Accep ed Oc obe 21, 2016 *To whom co espondence should be add essed. Tel: +39 049 827 6269; Email: sil io. osa[email p o ec ed] Co espondence may also be add essed o Sonia Longhi. Tel: +33 4 91 82 55 80; Email: Sonia.Longhi@a mb.uni -m s. Co espondence may also be add essed o Pe e Tompa. Tel: +32 2 629 1962; Email: p ompa@ ub.ac.be †These au ho s con ibu ed equally o he pape as i s au ho s. C The Au ho (s) 2016. Published by Ox o d Uni e si y P ess on behal o Nucleic Acids Resea ch. This is an Open Access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (h p://c ea i ecommons.o g/licenses/by-nc/4.0/), which pe mi s non-comme cial e-use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal wo k is p ope ly ci ed. Fo comme cial e-use, please con ac jou nals.pe [email protected] D220 Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue ABSTRACT The Da abase o P o ein Diso de (DisP o , URL: www.disp o .o g) has been signi ican ly upda ed and upg aded since i s las majo enewal in 2007. The cu en elease holds in o ma ion on mo e han 800 en ies o IDPs/IDRs, i.e. in insically diso de ed p o- eins o egions ha exis and unc ion wi hou a well-de ined h ee-dimensional s uc u e. We ha e e-cu a ed p e ious en ies o pu ge DisP o om con lic ing cases, and also upg aded he unc ional classi ica ion scheme o e lec con inuous ad ance in he ield in he pas 10 yea s o so. We de ine IDPs as p o eins ha a e diso de ed along hei en- i e sequence, i.e. en i ely lack s uc u al elemen s, and IDRs as egions ha a e a leas i e consecu- i e esidues wi hou well-de ined s uc u e. We base ou assessmen o diso de s ic ly on expe imen- al e idence, such as X- ay c ys allog aphy and nu- clea magne ic esonance (p ima y echniques) and a b oad ange o o he expe imen al app oaches (seconda y echniques). Con iden and ambiguous anno a ions a e highligh ed sepa a ely. DisP o 7.0 p esen s classi ied knowledge ega ding he expe - imen al cha ac e iza ion and unc ional anno a ions o IDPs/IDRs, and is in ended o p o ide an in alu- able esou ce o he esea ch communi y o a be e unde s anding s uc u al diso de and o de eloping be e compu a ional ools o s udying diso de ed p o eins. INTRODUCTION Ou adi ional iew o p o ein s uc u e and unc ion is deeply oo ed in he s uc u e– unc ion pa adigm which s a ed ha he polypep ide chain o p o eins needs o old in o a s able h ee-dimensional (3D) s uc u e, which is a p e equisi e o he unc ioning o he p o ein. The ex- eme explana o y powe and success o his model is a - es ed by mo e han hund ed housand high- esolu ion s uc u es in he P o ein Da a Bank (PDB) (1) and many Nobel P izes awa ded o desc ibing s uc u es cen al o unde s anding impo an cell-biological phenomena. I has been sugges ed almos 20 yea s ago, howe e , ha many p o eins o egions o p o eins in a ious p o eomes lack such s able 3D s uc u e, and a e a he in insically dis- o de ed unde na i e, physiological-like condi ions ( hus named IDPs/IDRs, espec i ely) (2–4). The ecogni ion o his s uc u al phenomenon b ough a adical change in he s uc u e– unc ion pa adigm, and c i ically ex ended he gene al app ecia ion o he ole o dynamics in p o ein unc- ion. I has been ecognized ha s uc u al diso de , which is p e alen in all o ganisms, plays oles p ima ily in cellula signaling and egula ion (5). Because o ha , IDPs/IDRs a e o en implica ed in diseases (6) and ep esen impo an d ug a ge s (7). The s uc u al and unc ional cha ac e iza ion o diso - de ed p o eins ep esen s a special challenge, because hey exis as an ensemble o apidly in e con e ing con o ma- ions. Al hough hey canno be c ys allized and hus can- no be di ec ly cha ac e ized by X- ay c ys allog aphy, he e a e a a ie y o echniques ha can epo on hei highly dynamic s uc u al s a e a low- o e en high spa ial and empo al esolu ion (3). The cu en bes s uc u al desc ip- ion o IDPs/IDRs is by s uc u al ensembles, which can be sol ed by a combina ion o expe imen al and compu a- ional app oaches and a e collec ed in o a dedica ed s uc- u al da abase, PED (8). S udies o he s uc u e– unc ion ela ionship o dis- o de ed p o eins ha e shown ha in ce ain cases hei unc ion a ises di ec ly om he diso de ed s a e (en opic chains), whe eas in many o he cases hei unc ion em- ana es om molecula ecogni ion accompanied by induced olding o speci ic binding pa ne s, such as ano he p o- ein, RNA o DNA molecule (9,10). In hese unc ions, he sensi i i y o egula ed emodeling o he diso de ed s uc- u al ensemble is an excellen subs a e o p o ein egula- ion, as exempli ied by equen pos - ansla ional modi i- ca ions (11) and special modes o allos e ic egula ion (12) in ol ing IDPs/IDRs. Due o he p e alence and impo ance o s uc u al diso - de , se e al dedica ed da abases co e ing a ious aspec s o IDPs/IDRs ha e appea ed in he pas decade. DisP o is he p ima y eposi o y o diso de - ela ed da a on sequence- and unc ional anno a ions, ocusing on diso de ed p o eins o egions wi h expe imen al e i ica ion (13,14). Se e al o he da abases a e based on p edic ions o diso de , such as D2P2, which con ains diso de p o ein p edic ions by a a ie y o p edic o s on 1765 comple e p o eomes (15), Mo- biDB, which ea u es h ee le els o anno a ions, manually cu a ed, indi ec and p edic ed o all UniP o sequences (o e 80 million) (16), and IDEAL, which con ains man- ual anno a ions o in e ac ion egions unde going induced olding, si es o pos - ansla ional modi ica ions and assign- men s o s uc u al domains (17). In addi ion, as al eady men ioned, PED is he da abase ha ga he s s uc u al in- o ma ion on IDPs/IDRs, in he o m o s uc u al ensem- bles (8). The in e ac ion o IDPs/IDRs wi h hei a ge (s) is mos o en media ed by sho con inuous s e ches o amino acids such as Molecula Recogni ion Elemen s/Fea u es (MoREs/MoRFs) (18) and sho /euka yo ic linea mo- i s (SLiMs/ELMs), which ha e been collec ed in he ELM da abase (19). Less equen ly, pa ne in e ac ions o IDPs/IDRs may also be media ed by in insically dis- o de ed domains (IDDs), i.e. longe egions ha con o m o he de ini ion o domains as unc ional, e olu iona y and s uc u al uni s (20). Al hough p obably s ill unde ap- p ecia ed, some o hese IDDs may be ound in he P am da abase o p o ein amilies which includes hei anno a- ions and unde lying mul iple sequence alignmen s (21). DisP o is cen al o all IDP- ela ed esea ch e o s, be- cause i collec s and p esen s in a s uc u ed way he co e expe imen al e idence epo ed o s uc u al diso de in p o eins. To gi e a new impe us o he ield, we ha e sig- ni ican ly upda ed and upg aded i wi h new ea u es. This new elease––DisP o 7.0––con ains mo e han 800 en ies o IDPs/IDRs. We ha e also e-de ined and ex ended unc- ional ca ego ies laying he basis o a unc ional on ology o IDPs, now encompassing 7 majo classes and 35 sub- classes, all based on published expe imen al da a. Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue D221 De ec ion and cha ac e iza ion o IDPs Technical ad ances in he ield o biophysical and s uc- u al biology in he las 50 yea s ha e p o ided he scien i ic communi y wi h an a senal o echniques o ackle he chal- lenging cha ac e iza ion o IDPs/IDRs (4,22). The a ious me hods di e in hei ex en o sophis ica ion, and hence in hei echnical demand, as well as in he na u e o he in o - ma ion hey p o ide. Nuclea magne ic esonance (NMR) and X- ay c ys allog aphy p o ide si e-speci ic in o ma ion, whe eas o he me hods p o ide mo e quali a i e and global in o ma ion (e.g. a -UV ci cula dich oism, size-exclusion ch oma og aphy; SEC). The ise o he ield o p o ein diso de has g ea ly ben- e i ed om s uc u al biology, because s uc u es deposi ed in he PDB (1) ha e been ins umen al o he de elopmen o diso de p edic o s, o en ained on egions o missing elec on densi y. De elopmen s o mul idimensional he - e onuclea NMR also enabled he s uc u al cha ac e iza- ion o diso de ed p o eins o inc easing size (23,24). In pa - icula , he e onuclea single quan um cohe ence (HSQC) expe imen s a e mos commonly used o de ine p o ein diso de i espec i e o whe he esidue-speci ic chemical shi s a e a ailable o no , as c owded HSQC spec a, cha - ac e ized by a poo sp ead o esonances, a e ypical o IDPs/IDRs. The same ea u e o low sp ead o p o on es- onances is also appa en in one-dimensional p o on-based NMR spec a, which o e s he ob ious ad an age o no e- qui ing iso opic labeling. Following assignmen o he spec- um, quan i a i e es ima ions o diso de can be ob ained h ough a ious NMR obse ables, such as chemical shi s, elaxa ion a es, esidual dipola couplings and esonance in ensi ies in pa amagne ic elaxa ion enhancemen expe - imen s. These da a enable p obing sequence-speci ic s uc- u al in o ma ion in IDPs/IDRs. A pa icula s eng h o NMR is ha i can be inc easingly applied unde uly in i o condi ions, in li e cells (25). The e o e, hese wo expe i- men al app oaches, X- ay c ys allog aphy and mul idimen- sional NMR, a e conside ed as he ‘p ima y echniques’ p o iding e idence o s uc u al diso de on a pe esidue basis in DisP o . I should no miss ou a en ion, hough, ha due o he expenses o iso opic labeling in NMR and he high a e o ailu e in p o ein c ys alliza ion, i would be un eason- able o only ely on hese wo app oaches o documen p o ein diso de . The e o e, beyond X- ay c ys allog aphy and NMR, a ple ho a o al e na i e biochemical and bio- physical app oaches ( e med ‘seconda y echniques’) p o- ide o hogonal in o ma ion on p o ein diso de in DisP o (4,22). The a ious app oaches a e o cou se no equi alen in e ms o eliabili y, esolu ion and accu acy and su e om speci ic d awbacks and limi a ions. S uc u al diso de is o en based on a -UV CD spec oscopy, which is o e all qui e eliable, bu does no enable disc imina ion be ween o de ed and mol en globula o ms. Nea -UV CD, beyond being able o un eil he lack o o de ed s uc u e, has he ad an age o dis inguishing be ween globula and mol en globule o ms. Ano he hallma k o diso de is anomalous sodium dodecyl sulpha e-polyac ylamide gel elec opho e- sis mig a ion, whe e IDPs ha e a high appa en molecula mass. IDPs/IDRs also beha e anomalously in SEC, ligh sca e ing (DLS, MALS), and in small-angle X- ay sca - e ing in ha hey display hyd odynamic adii (RH) and adii o gy a ion (Rg) highe han expec ed, e lec ing an ex ended con o ma ion. Fluo escence spec oscopy is ano he common me hod o assess diso de . In insic luo escence p obing he chem- ical en i onmen o yp ophan esidues p o ides in o ma- ion abou hei sol en -accessibili y, whe eas he mal di - e en ial scanning luo ime y––simila o di e en ial scan- ning calo ime y––can highligh he lack o a coope a i e he mal ansi ion and hence absence o o de ed s uc u e. Fluo escence esonance ene gy ans e be ween ex e nal luo opho es can e en gene a e in o ma ion on dis ance dis- ibu ions and help sol e he s uc u al ensemble o he IDP (26). Hype -sensi i i y o p o eolysis is also commonly used o map ou diso de ed egions o p o eins. Recen ly, na i e mass spec ome y exploi ing nano-elec osp ay ioniza ion (27,28) and high-speed a omic o ce mic oscopy ope a ing a he single-molecule le el (29) ha e eme ged as a ac i e al e na i es o add ess s uc u al diso de . As a las s a emen , i is no ewo hy ha he highe he numbe o independen expe imen al lines suppo ing dis- o de , he highe he eliabili y o he anno a ion. Fu he - mo e, mul i-dimensional in o ma ion may help ealize ha s uc u al diso de is no a single homogeneous s uc u al s a e along an o de -diso de bina y classi ica ion coo di- na e, i a he ep esen s a con inuum o s a es om he ully o de ed o he ully diso de ed. Simila ly, many examples o biological ele an diso de in agmen s ha a e missing om he ull leng h p o ein ha e been epo ed. Fu he - mo e, nume ous unc ional examples o ‘condi ional diso - de ’, i.e. ins ances whe e a diso de ed egion unc ions by ansi ions o o om a olded s a e (30), o when diso - de is only obse ed in a ac ion o simila s uc u es (31), lead o ambigui y and clea ly poin s o he need o ca - ying ou complemen a y expe imen s. In addi ion, an ex- eme case leading o con lic ing esul s is ep esen ed by ins ances whe e a p o ein egion, p edic ed o be o de ed, is no de ined in he elec on densi y in one c ys al s uc u e while being o de ed in ano he one ( o an example see (32) and DisP o en y DP00133). Do hese ambiguous egions ep esen a new class o diso de ha escape de ec ion us- ing he cu en ly a ailable diso de p edic o s ( hus se ing he scene o hei imp o emen ), o a con a io a e hey he esul o s a ic diso de ha a ises om expe imen al condi- ions o domain wobbling? Combining in o ma ion om a a ie y o sou ces may help cla i y hese cases and also im- p o e meaning ul desc ip ions o IDPs as con o ma ional ensembles (33,34), which may lead o u u e desc ip ions o he s uc u e– unc ion ela ionship o IDPs. Da abase s uc u e and implemen a ion Da abase eco ds. The echnology o DisP o has been up- da ed and is now based on a documen -o ien ed MongoDB da abase. S o ed documen s a e o wo ypes, ‘p o ein’ in- cluding gene al in o ma ion abou he p o ein and ‘diso - de ed egion (DR)’ including e idence o diso de om li - e a u e. P o ein in o ma ion is e ie ed om UniP o and includes clea age si es and chain/pep ide bounda ies o polyp o eins and p ocessed p o eins. DisP o is sequence- D222 Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue Figu e 1. DisP o sample en y, human p53 p o ein (DP00086). Se e al expe imen s ha e been ca ied ou o cha ac e ize he human p53 p o ein. DisP o epo s li e a u e e idence o IDRs. In pa icula , 11 di e en IDR e idences (Region E idences) ha e been collec ed om nine di e en pape s by wo di e en cu a o s. Mos o hese a e ela ed o he N- e minus and come om di e en ypes o expe imen s (Diso de Region De ails). Diso de egions and he numbe o DisP o e idences, sepa a ed in o con iden and ambiguous anno a ions, can be compa ed wi h s uc u al in o ma ion om he P am and MobiDB da abases in he Diso de O e iew. DisP o also p o ides unc ion anno a ion o IDRs by epo ing molecula unc ion, ansi ion and pa ne e ms (Func ional Anno a ion). A li e a u e e e ence is p o ided o each anno a ed IDR, linked o he ele an PubMed en y. Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue D223 cen ic and di e en iso o ms co espond o di e en en- ies as in he p e ious e sion. Clea ed p o eins a e me ged in o a single en y as hey a e p oduc s o he same na i e sequence. DisP o accession numbe s now ollow a single o ma and all p e ious en ies wi h a ‘ xxx’ su ix we e e- mo ed. DR eco ds a e e idence-cen ic, i.e. di e en docu- men s a e s o ed o di e en expe imen s e en when ela ed o he same egion. Fo cing a one- o-one pa adigm allows o ack anno a ion e idence ype and he co esponding li e a u e sou ce unambiguously. DR eco ds also include expe imen al e idence quali y ags o ambiguous anno a- ions. Some imes expe imen s a e ca ied ou on enginee ed sequences o agmen s which may p o e ambiguous o gen- e alize o he en i e sequence (AMBSEQ). Mo eo e , dis- o de bounda ies a e occasionally no clea om he li e - a u e (AMBLIT) o expe imen s a e pe o med unde ex- emely non-physiological condi ions (AMBEXP). The ma- jo imp o emen om p e ious e sions is he manually cu- a ed unc ional anno a ion o he egions. Whene e pos- sible, cu a o -associa ed unc ions based on li e a u e e i- dence a e indica ed by selec ing e ms om a new on ol- ogy buil o desc ibing diso de - ela ed unc ional modes. I none o he cu en e ms in he new on ology gi e a p ope desc ip ion o he unc ional mode, he cu a o may p opose a new e m o be added o he on ology. Accep ance o he new e m will equi e app o al by he IDP/IDR on- ology commi ee. Anno a ion pipeline. The new DisP o da a ha e been gen- e a ed by a communi y e o h ough a web se e in e ace accessible upon egis a ion. The same in as uc u e can be used bo h o c ea e and upda e en ies. Cu a o s p o ide an anno a ion h ough a submission o m whe e all ields a e alida ed on he clien -side and a sequence iewe allows he compa ison o assigned egions wi h s uc u e in o ma ion (P am domains, MobiDB diso de ). O no e, he name o he cu a o is clea ly isible in he en y o allow p ope a - ibu ion o c edi . The pipeline is ully au oma ic and can be po en ially applied o he en i e UniP o da abase. The DisP o public da abase is a snapsho o he communi y an- no a ions. En y page. The en y page ea u es ou di e en sec- ions (Figu e 1). A p o ein in o ma ion able gi es he p o- ein name, gene, synonyms, iden i ie s, axonomy and ‘ho- mologous’ en ies in e ed om sequence simila i y. An in- e ac i e ea u e iewe epo s DisP o diso de egions sepa a ed in o con iden and ambiguous anno a ions, col- o ed b own o in insically diso de ed egions and pu ple o con ex -dependen egions. P am domains along wi h PDB and p edic ed diso de de i ed om MobiDB a e also shown. Below, a de ailed ea u e iewe p o ides di e en isualiza ion laye s o highligh di e en unc ional aspec s (on ology e ms) and he s eng h o a ailable diso de e - idence. Each posi ion in he sequence is colo ed acco ding o he numbe and ype o e idence. Las bu no leas , he ull cu a o -gene a ed lis o egion e idences is epo ed on he bo om o he page and can be il e ed by selec ing an elemen ( egion) in he ea u e iewe . Figu e 1shows he cu en DisP o anno a ion o he human p53 p o ein. The combina ion o DisP o and PDB anno a ion clea ly shows how p53 con ains se e al segmen s unde going diso de o o de ansi ions. E idence o diso de om he li e a u e in he cen al p53 DNA binding domain, o which many c ys al s uc u es a e a ailable in he PDB, is ambiguous and highligh ed wi h AMBLIT. Simila con lic s can p ob- ably be ound in sco es o DisP o en ies and demons a e he impo ance o lagging ambiguous da a. B owsing and sea ching da a. Bo h b owsing and sea ch- ing unc ionali ies a e p o ided in a single solu ion om he ‘B owse’ page. A so able, cus omizable and il e able able lis s all en ies by p o ein. Al e na i ely, ano he able lis ing all egions is a ailable and accessible h ough he ‘ e- gions’ bu on. Complex que ies can be simula ed applying di e en il e s o di e en columns. Speci ic en ies can be selec ed manually and cus omized iews can be gene a ed by adding o emo ing columns. Fil e ed and/o selec ed da a can be downloaded bo h in ex and JSON o ma s. Al e na i ely, he ‘Sea ch’ page allows he use o sea ch o speci ic wo ds in a ee- ex o m o o sea ch o DisP o en- ies simila o a que y sequence. Ou pu o ei he sea ch is a p o ided in a simpli ied o m. Feedback page. DisP o use s a e highly encou aged o sugges addi ional diso de anno a ions o changes o ex- is ing anno a ions using he ‘Feedback’ page. This con ains a d op-down menu guiding he choice o eedback p o ided (e.g. websi e expe ience, no el anno a ions) and a message ield. Fo eedback ela ed o da a en ies, he use is asked o p o ide ei he he UniP o o DisP o ID and (whe e pos- sible) a PubMed e e ence. All messages a e e iewed by he cu a o s and in eg a ed in he da abase as ime pe mi s. Web echnology. The DisP o se e is implemen ed in Node.js (h ps://nodejs.o g) using he REST (Rep esen a- ional S a e T ans e ) a chi ec u e. The da a can be accessed h ough he web in e ace o p og amma ically exploi - ing he REST ul unc ionali y. Please e e o he ‘Help’ sec ion o he websi e o de ails on using he DisP o web se ices. The web in e ace is buil using Angula .js (h ps://angula js.o g) and Boo s ap (h p://ge boo s ap. com) amewo ks. The ea u e iewe is implemen ed on op o he Bio.js lib a y. Da abase con en : upg ades and upda es En ies in DisP o 7.0 came om h ee majo sou ces: (i) om he p e ious e sion o DisP o (whe e con lic ing cases ha e been e-anno a ed), (ii) no el cases iden i ied as PDB en ies wi h long egions o missing elec on densi y and (iii) p o eins iden i ied by ex -mining in PubMed ab- s ac s o keywo ds ‘in insically diso de ed’, ‘in insically uns uc u ed’ and ‘s uc u al diso de ’. New p o eins se- lec ed based on diso de con en (es ima ed based on Mo- biDB da a) we e p io i ized (i app op ia e in o ma ion was a ailable in SwissP o ) o concen a e on well-s udied and mos in e es ing cases. New p o eins we e also selec ed by cu a o s hemsel es o exploi hei speci ic p e ious knowl- edge. All en ies om p e ious e sions we e e-anno a ed o emo e inconsis encies. One hund ed and nine y-eigh p e ious en ies we e comple ely emo ed and 469 modi- ied. Recu ing p oblems being ixed we e w ong o ganism D224 Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue Table 1. DisP o anno a ion con en Me hod/ unc ion P o eins Regions Residues Nuclea magne ic esonance (NMR) 333 592 32 926 X- ay c ys allog aphy 326 683 20 742 Ci cula dich oism (CD) spec oscopy, a -UV 261 352 53 935 Sensi i i y o p o eolysis 75 95 13 961 Size exclusion/gel il a ion ch oma og aphy 62 67 12 206 P o on-based NMR 53 69 7723 SDS-PAGE gel, abe an mobili y on 34 34 6326 O he me hods 237 273 41 833 Diso de ansi ion 564 1505 151 498 Molecula unc ion 489 1199 106 670 Molecula pa ne 444 1108 119 665 Dis ibu ion o DisP o anno a ion based on expe imen al e idence (me hod) and diso de unc ion ( unc ion). As each anno a ed diso de egion co e- sponds o one piece o expe imen al e idence, mul iple egions can map o he same sequence segmen . I a p o ein is anno a ed mul iple imes wi h he same ype o expe imen i is coun ed once. The numbe o esidues is he sum o egion leng hs. Figu e 2. Dis ibu ion o diso de segmen leng hs. Segmen leng hs a e binned in g oups o 10 esidues, e.g. he column 10 showing leng hs be ween 10 and 19 esidues. The cu en DisP o elease is dis inguished by expe imen al echnique (X- ay in g een, NMR in blue and o he me hods in ed). The p e ious DisP o elease is shown in a single g ay ba as i did no ha e he expe imen al echnique in a machine- eadable o ma . o iso o m assignmen s, w ong IDR posi ioning, un acked diso de e idence (e.g. missing explici li e a u e e e ence) and weak e idence (e.g. based on e y sho agmen s, please no e ha he minimal leng h o an IDR in DisP o 7.0 is 5 esidues). Mo eo e , diso de anno a ions based on no aceable au ho /cu a o s a emen s we e disca ded. Whe e necessa y, a cu a o commen now highligh s c i icisms el- a i e o a gi en e idence/expe imen , e.g. i he expe imen has been ca ied ou on an enginee ed p o ein. Regions anno a ed as s uc u ed in p e ious DisP o eleases we e emo ed (33 egions). In o ma ion ela ed o expe imen s has been simpli ied by skipping echnical de ails ega ding expe imen al condi ions. Howe e , weak expe imen al e i- dence is il e ed ou by he cu a o du ing anno a ion and agged wi h one o h ee ambiguous labels. O e all, DisP o 7.0 includes 804 en ies and 2167 diso de ed egions, wi h a o al o 92 432 amino acids wi h clea expe imen al and unc ional anno a ions (Table 1), and he leng h dis ibu- ion o diso de ed egions has signi ican ly changed om he las elease o DisP o (Figu e 2). New ea u e: unc ional classi ica ion IDPs/IDRs ca y ou impo an unc ions in he cell. The ield has se led on he no ion ha s uc u al diso de ep- esen s a con inuum o s a es om ully olded o ully un- olded ( andom coil-like), and unc ion may come om any o he s a es and ansi ions be ween hem. Tha is, hei unc ion may come di ec ly om he diso de ed s a e o om molecula ecogni ion and binding o pa ne molecule(s). We de i e ou classi ica ion om he logic o he gene on ology classi ica ion scheme (35), which is based on h ee s uc u ed on ologies asc ibing unc ional e ms o gene p oduc s (p o eins) in e ms o hei associa ed biolog- ical p ocesses (BP), cellula componen s (CC) and molecu- la unc ions (MF). Appa en ly, he CC and BP on ologies do no depend on he diso de ed s a us o he p o ein, hey Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue D225 Table 2. Majo unc ional ca ego ies o he MFUN on ology o DisP o MFUN code Gene ic unc ional ca ego y Func ional ca ego y MFUN 01 En opic chain Flexible linke /space En opic b is le En opic clock En opic sp ing S uc u al mo a Sel - anspo h ough channel MFUN 02 Molecula ecogni ion: assemble Assemble Localiza ion ( a ge ing) Localiza ion ( e he ing) P ion (sel -assembly, polyme iza ion) Liquid-liquid phase sepa a ion/demixing (sel -assembly) MFUN 03 Molecula ecogni ion: sca enge Neu aliza ion o oxic molecules Me al binding/me al sponge Wa e s o age MFUN 04 Molecula ecogni ion: e ec o Inhibi o Disassemble Ac i a o cis- egula o y elemen s (inhibi o y modules) DNA bending DNA unwinding MFUN 05 Molecula ecogni ion: display si e Phospho yla ion Ace yla ion Me hyla ion Glycosyla ion Ubiqui ina ion Fa y acyla ion (my is ola ion and palmi oyla ion) Limi ed p o eolysis MFUN 06 Molecula ecogni ion: chape one P o ein de e gen /sol a e laye Space illing En opic exclusion En opy ans e The unc ional schemes a e an open hie a chy. One goal o sha ing in o ma ion wi h he communi y h ough DisP o is o e ine ou iews o he unc ional modes o IDPs. simply e lec he in acellula loca ion o he p o ein and he BP i pa icipa es in, which can be kep wi hou e e - ence o he diso de ed s a us (35). The si ua ion is en i ely di e en wi h MF, which desc ibes he elemen al ac i i ies o a p o ein a he molecula le el. In his ega d, IDPs basi- cally di e om olded p o eins, such as enzymes o ligand- binding ecep o s, because hei mode o ac ion and ype o unc ion a e usually comple ely di e en om hose o olded p o eins. The e o e, we ha e de eloped a no el classi- ica ion scheme ha me ges and expands p e ious schemes ha sugges ed hi y (36)andsix(9) di e en ca ego ies, o p o ide classi ied desc ip o s o hei MFs. Because p e- ious ca ego ies (9,36) lacked cohe ence ( o example, hey ea ed s uc u al ansi ions and in e ac ion pa ne s a he same le el), we c ea ed a a ional scheme ha dis inguishes hese di e en ypes o on ologies (c . Table 2and e . (3)). The h ee sub-on ologies a e as ollows: (i) molecula unc ion o diso de (MFUN): desc ibes he ype o unc- ional eadou o unc ion (such as molecula chape one); (ii) molecula ansi ion (TRAN) necessa y o unc ion (such as diso de - o-o de ansi ion); and (iii) molecula pa ne (PART) ha is ecognized by he diso de ed p o ein (such as p o ein/RNA/DNA/small molecule). The MFUN on ology is desc ibed in de ail in Table 1. The TRAN on- ology can be u he simpli ied o wo IDR s a es (diso de and ansi ion) o highligh di e en ypes o beha io , e.g. in he ea u e iewe o each DisP o en y. CONCLUSIONS AND FUTURE WORK We ha e p esen ed an upda ed and comple ely e-wo ked e sion o he DisP o da abase. I now ea u es s a e-o - he-a da abase and web echnology, enabling p og am- ma ic access o in e es ed pa ies. The con en was ex- panded by de ining a s anda dized se o expe imen al ech- niques and a no el unc ional on ology o diso de ed seg- men s. Bo h allow o a iche desc ip ion o diso de which may be used o u he analyses. The o he main imp o e- men in DisP o is a comple e e-anno a ion o exis ing en- ies o emo e inconsis encies and an expansion o ca. 50% o e he p e ious elease, which also esul ed in a signi i- can shi in he leng h co e age o diso de ed egions in he da abase. This ad ance was made possible by a dis ibu ed anno a ion e o coo dina ed by he COST Ac ion NGP- ne (URL: ngp-ne .bio.unipd.i ) in ol ing a dozen di e en g oups and close o 40 anno a o s. The longe e m main- enance o DisP o is p o ided by he I alian node o he Eu opean bioin o ma ics in as uc u e Elixi . In he u u e we hope ha DisP o can be able o p o ide diso de anno- a ions o UniP o . Finally, we hope ha he upg ade o DisP o will encou - age he scien i ic communi y o deposi expe imen al e i- dence o diso de wi hin his unique eposi o y, and ha his enewed momen um will lead o an inc eased awa eness o he impo ance o in insic diso de in p o eins. D226 Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue FUNDING COST Ac ion BM1405 NGP-ne ; ELIXIR-IIB (elixi - i aly.o g); ‘Lend¨ule ’ G an om he Hunga ian Academy o Sciences [LP2014-16 o Z.D.]; Hunga ian Scien i ic Re- sea ch Fund [OTKA K 108798 o Z.D.]; AIRC Resea ch Fellowship ( o D.P.); Spanish Minis e io de Educaci´ on Cul- u a i Depo e PhD Fellowship ( o J.P.); Mexican Na- ional Council o Science and Technology (CONACYT) PhD Fellowship [215503 o M.M.-C.]; G an Po oNeu- oDRI e@i3S unded by No e Po ugal Regional Ope a- ional P og amme (NORTE 2020), unde he PORTUGAL 2020 Pa ne ship Ag eemen , h ough he Eu opean Re- gional De elopmen Fund (ERDF) ( o S.M.-R.); Di ec ion G´ en´ e ale des A m´ ees and Aix-Ma seille Uni e si y PhD Fellowship ( o E.Sa.); OTKA G an [PD-OTKA 108772 o E.Sc.]; F ench Minis y o Na ional Educa ion, Resea ch and Technology PhD Fellowship ( o A.S.); Minis y o Ed- uca ion, Science and Technological De elopmen o he Re- public o Se bia [173001, 173049 o N.V., R.D.]; ICREA- Academia Awa d ( o S.V.); Odysseus G an om Resea ch Founda ion Flande s (FWO) [G.0029.12 o P.T.]; AIRC IG G an [17753 o S.T., in pa ]; I alian Minis y o Heal h [GR-2011-02347754 o E.L., S.T.; GR-2011-02346845 o S.T.]; Swedish Resea ch Council G an [VR-NT 2012-5046 o A.E.]. 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