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Intrinsically Disordered Proteins: An Update

A. Keith Dunker, Christopher J. Oldfield, Jingwei Meng, Pedro Romero, Jack Y. Yang, Zoran Obradovic, Vladimir N. Uversky
2007 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering  
At the algorithmic level, prediction of protein intrinsic disorder is similar to the prediction of secondary structure, but, at the structural level, secondary structure and intrinsic disorder are entirely  ...  Just over 10 years ago, in June, 1997, in the Proceedings of the IEEE International Conference on Neural Networks, we published our first predictor of intrinsically disordered protein [1].  ...  Since the 1970s, an increased stream of disordered protein examples has been reported, and many of these are described in our database of intrinsically disordered proteins [9, 10] .  ... 
doi:10.1109/bibe.2007.4375544 dblp:conf/bibe/DunkerOMRYOU07a fatcat:y6jmvrcsmbcxfmekbgxowrgtie

The unfoldomics decade: an update on intrinsically disordered proteins

A Keith Dunker, Christopher J Oldfield, Jingwei Meng, Pedro Romero, Jack Y Yang, Jessica Chen, Vladimir Vacic, Zoran Obradovic, Vladimir N Uversky
2008 BMC Genomics  
On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function.  ...  While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different.  ...  an abundance of intrinsic disorder in diseaserelated proteins [38, [67] [68] [69] [70] [71] [72] [73] [74]  ... 
doi:10.1186/1471-2164-9-s2-s1 pmid:18831774 pmcid:PMC2559873 fatcat:2hhpzzrc3bcxthl4uqimvksnce

MobiDB: intrinsically disordered proteins in 2021

Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Mičetić, Federica Quaglia, Lisanna Paladin, Pathmanaban Ramasamy, Zsuzsanna Dosztányi, Wim F Vranken, Norman E Davey (+3 others)
2020 Nucleic Acids Research  
The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins.  ...  Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process.  ...  INTRODUCTION Intrinsically disordered regions (IDRs) of proteins do not adopt a highly populated structure in isolation, but sample a wide range of conformations.  ... 
doi:10.1093/nar/gkaa1058 pmid:33237329 fatcat:fpb77lr37naaxopskkh2rq7s3e

Databases for intrinsically disordered proteins

Damiano Piovesan, Alexander Miguel Monzon, Federica Quaglia, Silvio C. E. Tosatto
2022 Acta Crystallographica Section D: Structural Biology  
Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation.  ...  Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories.  ...  Intrinsically disordered proteins Acta Cryst. (2022). D78  ... 
doi:10.1107/s2059798321012109 pmid:35102880 pmcid:PMC8805306 fatcat:vw6hs7avpnay3jahmqiiev4hsu

Quarterly intrinsic disorder digest (January-February-March, 2014)

Shelly DeForte, Krishna D. Reddy, Vladimir N. Uversky
2016 Intrinsically Disordered Proteins  
intrinsic disorder).  ...  This is the 5 th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins.  ...  PAGE4 is an intrinsically disordered stress-response protein that is aberrantly expressed in cancer.  ... 
doi:10.1080/21690707.2016.1153395 pmid:28232896 pmcid:PMC5314902 fatcat:ifedvhbbqrftpdg55ckynkpusi

Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013)

Shelly DeForte, Krishna D Reddy, Vladimir N Uversky
2015 Intrinsically Disordered Proteins  
This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins.  ...  The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic  ...  for intrinsically disordered proteins.  ... 
doi:10.4161/21690707.2014.984569 pmid:28293487 pmcid:PMC5336282 fatcat:dx73jnazg5f6znfezgsedtctwe

DisProt: intrinsic protein disorder annotation in 2020

2019 Nucleic Acids Research  
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature.  ...  Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website.  ...  Part of this work was done in the context of an ELIXIR Implementation Study linked to the ELIXIR Data platform.  ... 
doi:10.1093/nar/gkz975 pmid:31713636 pmcid:PMC7145575 fatcat:kldsrbqw2nhw3evs6c53a7hdi4

Intrinsic Disorder in Putative Protein Sequences

Uros Midic, Zoran Obradovic
2011 2011 IEEE International Conference on Bioinformatics and Biomedicine  
In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins.  ...  Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro.  ...  Background Intrinsically disordered proteins (IDPs) are proteins that lack stable tertiary structure under physiological conditions in vitro [1] .  ... 
doi:10.1109/bibm.2011.32 dblp:conf/bibm/MidicO11 fatcat:uoxtsu5udzb3hpq24zh3nqb2a4

Intrinsic disorder in putative protein sequences

Uros Midic, Zoran Obradovic
2012 Proteome Science  
In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins.  ...  Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro.  ...  Background Intrinsically disordered proteins (IDPs) are proteins that lack stable tertiary structure under physiological conditions in vitro [1] .  ... 
doi:10.1186/1477-5956-10-s1-s19 pmid:22759577 pmcid:PMC3380756 fatcat:pieahwzzxrfjvdl3tt37x5wew4

Digested disorder

Shelly DeForte, Krishna D Reddy, Vladimir N Uversky
2013 Intrinsically Disordered Proteins  
Intrinsically Disordered Proteins journal.  ...  with intrinsically disordered proteins.  ... 
doi:10.4161/idp.27454 pmid:28516028 pmcid:PMC5424790 fatcat:dx2e5o56gvefrn72xoa3rw35ly

An intrinsically disordered proteins community for ELIXIR

Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas (+32 others)
2019 F1000Research  
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation.  ...  The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua.  ...  The field is on the cusp of an era where the high-throughput characterisation of the extensive intrinsically disordered regions (IDRs) of proteins is possible.  ... 
doi:10.12688/f1000research.20136.1 pmid:31824649 pmcid:PMC6880265 fatcat:2rw2z5q3obgrllxjcthcqgoiyu

IMPROVING SEQUENCE ALIGNMENTS FOR INTRINSICALLY DISORDERED PROTEINS

PREDRAG RADIVOJAC, ZORAN OBRADOVIC, CELESTE J. BROWN, A. KEITH DUNKER
2001 Biocomputing 2002  
Here we analyze sequence alignments for intrinsically disordered proteins.  ...  Results show an improvement in the ability to detect and discriminate related disordered proteins whose average sequence identity with the other family members is below 50%.  ...  Chris Oldfield, Sachiko Takayama and others did yeoman's work in developing the database proteins with physically characterized regions of intrinsic disorder.  ... 
doi:10.1142/9789812799623_0055 fatcat:xs65j4rirfgvnfibxxg7cxddam

Predicting intrinsic disorder in proteins: an overview

Bo He, Kejun Wang, Yunlong Liu, Bin Xue, Vladimir N Uversky, A Keith Dunker
2009 Cell Research  
The discovery of intrinsically disordered proteins (IDP) (i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures) came as an unexpected surprise, as the existence  ...  Accurate prediction of a protein's predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function,  ...  Intrinsic disorder in a given protein can be found by multiple experimental and computational techniques.  ... 
doi:10.1038/cr.2009.87 pmid:19597536 fatcat:3meuomgupjegbop5gqkdzqacwq

MFDp2

Marcin J. Mizianty, Zhenling Peng, Lukasz Kurgan
2013 Intrinsically Disordered Proteins  
*PrDos and PreDisorder failed to predict the DP00623 protein; the evaluation is based on the remaining 104 chains. e24428-4 Intrinsically Disordered Proteins Volume 1 5-15 min for an average size protein  ...  Introduction The intrinsically disordered proteins (IDPs), also called intrinsically unstructured or natively unfolded, are either entirely disordered or contain disordered regions in their native state  ... 
doi:10.4161/idp.24428 pmid:28516009 pmcid:PMC5424793 fatcat:uhecuture5hp7b4fipaga7aira

PreSMo Target-Binding Signatures in Intrinsically Disordered Proteins

Do-Hyoung Kim, Kyou-Hoon Han
2018 Molecules and Cells  
Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions.  ...  To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution.  ...  Intrinsically unstructured/unfolded proteins (IUPs), now more commonly known as intrinsically disordered proteins (IDPs) (Dunker et al., 2013) , are very peculiar proteins that do not form well-folded  ... 
doi:10.14348/molcells.2018.0192 pmid:30352491 pmcid:PMC6199570 fatcat:rl47fcb7urcmpn7oc5h4jtfzry
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