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
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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.]. Compu a ional esou ces we e p o ided by he
Swedish Na ional In as uc u e o Compu ing (SNIC)
a NSC. Funding o open access cha ge: COST Ac ion
BM1405 NGP-ne .
Con lic o in e es s a emen . None decla ed.
REFERENCES
1. Be man,H.M., Wes b ook,J., Feng,Z., Gilliland,G., Bha ,T.N.,
Weissig,H., Shindyalo ,I.N. and Bou ne,P.E. (2000) The p o ein da a
bank. Nucleic Acids Res.,28, 235–242.
2. Old ield,C.J. and Dunke ,A.K. (2014) In insically diso de ed
p o eins and in insically diso de ed p o ein egions. Annu. Re .
Biochem.,83, 553–584.
3. an de Lee,R., Buljan,M., Lang,B., Wea he i ,R.J.,
Daughd ill,G.W., Dunke ,A.K., Fux ei e ,M., Gough,J., Gspone ,J.,
Jones,D.T. e al. (2014) Classi ica ion o in insically diso de ed
egions and p o eins. Chem. Re .,114, 6589–6631.
4. Habchi,J., Tompa,P., Longhi,S. and U e sky,V.N. (2014) In oducing
p o ein in insic diso de . Chem. Re .,114, 6561–6588.
5. Xie,H., Vuce ic,S., Iakouche a,L.M., Old ield,C.J., Dunke ,A.K.,
U e sky,V.N. and Ob ado ic,Z. (2007) Func ional an hology o
in insic diso de . 1. Biological p ocesses and unc ions o p o eins
wi h long diso de ed egions. J. P o eome Res.,6, 1882–1898.
6. U e sky,V.N., Old ield,C.J. and Dunke ,A.K. (2008) In insically
diso de ed p o eins in human diseases: in oducing he D2 concep .
Annu. Re . Biophys.,37, 215–246.
7. Me allo,S.J. (2010) In insically diso de ed p o eins a e po en ial
d ug a ge s. Cu . Opin. Chem. Biol.,14, 481–488.
8. Va adi,M., Kosol,S., Leb un,P., Valen ini,E., Blackledge,M.,
Dunke ,A.K., Felli,I.C., Fo man-Kay,J.D., K iwacki,R.W.,
Pie a elli,R. e al. (2014) pE-DB: a da abase o s uc u al ensembles
o in insically diso de ed and o un olded p o eins. Nucleic Acids
Res.,42, D326–D335.
9. Tompa,P. (2005) The in e play be ween s uc u e and unc ion in
in insically uns uc u ed p o eins. FEBS Le .,579, 3346–3354.
10. W igh ,P.E. and Dyson,H.J. (2009) Linking olding and binding.
Cu . Opin. S uc . Biol.,19, 31–38.
11. Iakouche a,L.M., Radi ojac,P., B own,C.J., O’Conno ,T.R.,
Sikes,J.G., Ob ado ic,Z. and Dunke ,A.K. (2004) The impo ance o
in insic diso de o p o ein phospho yla ion. Nucleic Acids Res.,32,
1037–1049.
12. Tompa,P. (2014) Mul is e ic egula ion by s uc u al diso de in
modula signaling p o eins: an ex ension o he concep o allos e y.
Chem. Re .,114, 6715–6732.
13. Vuce ic,S., Ob ado ic,Z., Vacic,V., Radi ojac,P., Peng,K.,
Iakouche a,L.M., Co ese,M.S., Lawson,J.D., B own,C.J., Sikes,J.G.
e al. (2005) DisP o : a da abase o p o ein diso de . Bioin o ma ics,
21, 137–140.
14. Sickmeie ,M., Hamil on,J.A., LeGall,T., Vacic,V., Co ese,M.S.,
Tan os,A., Szabo,B., Tompa,P., Chen,J., U e sky,V.N. e al. (2007)
DisP o : he Da abase o Diso de ed P o eins. Nucleic Acids Res.,35,
D786–D793.
15. Oa es,M.E., Rome o,P., Ishida,T., Ghalwash,M., Mizian y,M.J.,
Xue,B., Dosz anyi,Z., U e sky,V.N., Ob ado ic,Z., Ku gan,L. e al.
(2013) D(2)P(2): da abase o diso de ed p o ein p edic ions. Nucleic
Acids Res.,41, D508–D516.
16. Po enza,E., Di Domenico,T., Walsh,I. and Tosa o,S.C. (2015)
MobiDB 2.0: an imp o ed da abase o in insically diso de ed and
mobile p o eins. Nucleic Acids Res.,43, D315–D320.
17. Fukuchi,S., Sakamo o,S., Nobe,Y., Mu akami,S.D., Amemiya,T.,
Hosoda,K., Koike,R., Hi oaki,H. and O a,M. (2012) IDEAL:
in insically diso de ed p o eins wi h ex ensi e anno a ions and
li e a u e. Nucleic Acids Res.,40, D507–D511.
18. Mohan,A., Old ield,C.J., Radi ojac,P., Vacic,V., Co ese,M.S.,
Dunke ,A.K. and U e sky,V.N. (2006) Analysis o molecula
ecogni ion ea u es (MoRFs). J. Mol. Biol.,362, 1043–1059.
19. Dinkel,H., Van Roey,K., Michael,S., Kuma ,M., Uya ,B.,
Al enbe g,B., Milche skaya,V., Schneide ,M., Kuhn,H., Beh end ,A.
e al. (2016) ELM 2016–da a upda e and new unc ionali y o he
euka yo ic linea mo i esou ce. Nucleic Acids Res.,44, D294–D300.
20. Tompa,P., Fux ei e ,M., Old ield,C.J., Simon,I., Dunke ,A.K. and
U e sky,V.N. (2009) Close encoun e s o he hi d kind: diso de ed
domains and he in e ac ions o p o eins. Bioessays,31, 328–335.
21. Finn,R.D., Coggill,P., Ebe ha d ,R.Y., Eddy,S.R., Mis y,J.,
Mi chell,A.L., Po e ,S.C., Pun a,M., Qu eshi,M.,
Sang ado -Vegas,A. e al. (2016) The P am p o ein amilies da abase:
owa ds a mo e sus ainable u u e. Nucleic Acids Res.,44,
D279–D285.
22. Rece eu -B echo ,V., Bou his,J.M., U e sky,V.N., Cana d,B. and
Longhi,S. (2006) Assessing p o ein diso de and induced olding.
P o eins,62, 24–45.
23. Kosol,S., Con e as-Ma os,S., Cedeno,C. and Tompa,P. (2013)
S uc u al cha ac e iza ion o in insically diso de ed p o eins by
NMR spec oscopy. Molecules,18, 10802–10828.
24. Felli,I.C. and Pie a elli,R. (2012) Recen p og ess in NMR
spec oscopy: owa d he s udy o in insically diso de ed p o eins o
inc easing size and complexi y. IUBMB Li e,64, 473–481.
25. Theille ,F.X., Binol i,A., Bekei,B., Ma o ana,A., Rose,H.M.,
S ui e ,M., Ve zini,S., Lo enz,D., an Rossum,M., Gold a b,D. e al.
(2016) S uc u al diso de o monome ic alpha-synuclein pe sis s in
mammalian cells. Na u e,530, 45–50.
26. Schule ,B., So anno,A., Ho mann,H. and Ne els,D. (2016)
Single-molecule FRET spec oscopy and he polyme physics o
un olded and in insically diso de ed P o eins. Annu. Re . Biophys.,
45, 207–231.
27. Kal asho ,I.A., Bobs ,C.E. and Abzalimo ,R.R. (2013) Mass
spec ome y-based me hods o s udy p o ein a chi ec u e and
dynamics. P o ein Sci.,22, 530–544.
28. Bo ysik,A.J., Ko acs,D., Guha oy,M. and Tompa,P. (2015) Ensemble
me hods enable a new de ini ion o he solu ion o gas-phase ans e
o in insically diso de ed p o eins. J. Am. Chem. Soc.,137,
13807–13817.
29. Miyagi,A., Tsunaka,Y., Uchihashi,T., Mayanagi,K., Hi ose,S.,
Mo ikawa,K. and Ando,T. (2008) Visualiza ion o in insically
diso de ed egions o p o eins by high-speed a omic o ce
mic oscopy. Chemphyschem,9, 1859–1866.
30. Jakob,U., K iwacki,R. and U e sky,V.N. (2014) Condi ionally and
ansien ly diso de ed p o eins: awakening c yp ic diso de o
egula e p o ein unc ion. Chem. Re .,114, 6779–6805.
31. DeFo e,S. and U e sky,V.N. (2016) Resol ing he ambigui y:
making sense o in insic diso de when PDB s uc u es disag ee.
P o ein Sci.,25, 676–688.
32. Blocquel,D., Habchi,J., Du and,E., Se ajol,M., Fe on,F., E ales,J.,
Papageo giou,N. and Longhi,S. (2014) Coiled-coil de o ma ions in
c ys al s uc u es: he measles i us phosphop o ein mul ime iza ion
Nucleic Acids Resea ch, 2017, Vol. 45, Da abase issue D227
domain as an illus a i e example. Ac a C ys allog . D Biol.
C ys allog .,70, 1589–1603.
33. S e ckx,Y.G., Volko ,A.N., V anken,W.F., K agelj,J., Jensen,M.R.,
Bu s,L., Ga cia-Pino,A., Jo e,T., Van Melde en,L., Blackledge,M.
e al. (2014) Small-angle X- ay sca e ing- and nuclea magne ic
esonance-de i ed con o ma ional ensemble o he highly lexible
an i oxin PaaA2. S uc u e,22, 854–865.
34. Aznau yan,M., Delgado,L., So anno,A., Ne els,D., Huang,J.R.,
Labha d ,A.M., G zesiek,S. and Schule ,B. (2016) Comp ehensi e
s uc u al and dynamical iew o an un olded p o ein om he
combina ion o single-molecule FRET, NMR, and SAXS. P oc. Na l.
Acad. Sci. U.S.A.,113, E5389–E5398.
35. Conso ium, G.O. (2015) Gene on ology conso ium: going
o wa d. Nucleic Acids Res.,43, D1049–D1056.
36. Dunke ,A.K., B own,C.J., Lawson,J.D., Iakouche a,L.M. and
Ob ado ic,Z. (2002) In insic diso de and p o ein unc ion.
Biochemis y,41, 6573–6582.