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A comprehensive assessment of long intrinsic protein disorder from the DisProt database

Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Peter Tompa, Silvio C E Tosatto, Alfonso Valencia
2017 Bioinformatics  
Supplementary The different DisProt subsets are listed with the number of proteins and residues attributed to each of the three classes (disorder, order, undefined) .  ...  The last three subsets are only viral proteins (virus), proteins annotated from X-ray and NMR (primary) and indirect biochemical experiments (secondary) methods. Figure S2 .  ... 
doi:10.1093/bioinformatics/btx590 pmid:28968848 fatcat:w7wrkpuqofhdpipdwsm6miesla

Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins

Akila Katuwawala, Lukasz Kurgan
2020 Biomolecules  
We review 28 surveys of disorder predictors, showing that only 11 include assessment of predictive performance. We identify and address a few drawbacks of these past surveys.  ...  This finding motivates the development of a new generation of methods that would target these difficult-to-predict disordered proteins.  ...  They include three versions of ESpritz that are tuned to predict intrinsic disorder annotated from X-ray structures (ESpritz-Xray), NMR structures (ESpritz-NMR) and using DisProt database (ESpritz-DisProt  ... 
doi:10.3390/biom10121636 pmid:33291838 fatcat:g2s4imb37zdrte6sl36emjowrm

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

Emilio Potenza, Tomás Di Domenico, Ian Walsh, Silvio C.E. Tosatto
2014 Nucleic Acids Research  
MobiDB (http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically disordered regions are key for the function of numerous proteins.  ...  The database features three levels of annotation: manually curated, indirect and predicted. Manually curated data is extracted from the DisProt database.  ...  The highest quality data is currently extracted from the DisProt database ( 6 ), a central repository manually curated for structure-function annotations associated with protein intrinsic disorder.  ... 
doi:10.1093/nar/gku982 pmid:25361972 pmcid:PMC4384034 fatcat:uougiyo3wjgodcgnkg3nqyi3fq

Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank

Alexander Miguel Monzon, Marco Necci, Federica Quaglia, Ian Walsh, Giuseppe Zanotti, Damiano Piovesan, Silvio C. E. Tosatto
2020 International Journal of Molecular Sciences  
Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the  ...  Intrinsically disordered protein regions are commonly defined from missing electron density in X-ray structures.  ...  On one hand, we assessed disorder predictors on LDRs present in a curated resource as DisProt database.  ... 
doi:10.3390/ijms21124496 pmid:32599863 fatcat:f7qazk5gnzeuhbjj4lwcntgrdy

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

Damiano Piovesan, Francesco Tabaro, Lisanna Paladin, Marco Necci, Ivan Mičetić, Carlo Camilloni, Norman Davey, Zsuzsanna Dosztányi, Bálint Mészáros, Alexander M Monzon, Gustavo Parisi, Eva Schad (+5 others)
2017 Nucleic Acids Research  
A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility  ...  Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases.  ...  ACKNOWLEDGEMENTS We acknowledge ELIXIR-IIB (elixir-italy.org), the Italian Node of the European ELIXIR infrastructure (elixireurope.org), for supporting the development and maintenance of MobiDB.  ... 
doi:10.1093/nar/gkx1071 pmid:29136219 pmcid:PMC5753340 fatcat:ctjxsg7edzee7mdg24psbx667u

There is Diversity in Disorder—"In all Chaos there is a Cosmos, in all Disorder a Secret Order"

Jakob T. Nielsen, Frans A. A. Mulder
2016 Frontiers in Molecular Biosciences  
The protein universe consists of a continuum of structures ranging from full order to complete disorder.  ...  With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small  ...  In addition, our analysis paints a validated picture of protein disorder for a diverse subset of 117 example proteins that are either classified as IDPs, or possess long intrinsically disordered regions  ... 
doi:10.3389/fmolb.2016.00004 pmid:26904549 pmcid:PMC4749933 fatcat:hgrdzzmfqbgmnnlrrsvqu6e4im

Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus

Xiao Fan, Lukasz Kurgan
2013 Journal of Biomolecular Structure and Dynamics  
Availability of computational methods that predict disorder from protein sequences fuels rapid advancements in the protein disorder field.  ...  We are first to comprehensively assess predictions in the context of several functional types of disorder and we demonstrate that disCoP generates accurate predictions of disorder located at the post-translational  ...  Acknowledgement The authors thank Mr. Marcin Mizianty for help with the implementation and testing of the disCoP_WS method.  ... 
doi:10.1080/07391102.2013.775969 pmid:23534882 fatcat:dd3x25cyozhunaok6avewzw6lq

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

Andrew Campen, Ryan Williams, Celeste Brown, Jingwei Meng, Vladimir Uversky, A. Dunker
2008 Protein Peptide Letters  
The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, A web-based server has been created to apply the TOP-IDP scale to predict intrinsically  ...  In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales.  ...  ACKNOWLEDGEMENTS This work was supported in part by the grants R01 LM007688-01A1 (to A.K.D and V.N.U.) and GM071714-01A2 (to A.K.D and V.N.U.) from the National Institutes of Health and the Programs of  ... 
doi:10.2174/092986608785849164 pmid:18991772 pmcid:PMC2676888 fatcat:sb5tmo3cezghxasrsxaserp3pa

Quality and bias of protein disorder predictors

Jakob T. Nielsen, Frans A. A. Mulder
2019 Scientific Reports  
Our analysis has important implications for the validity and the interpretation of protein disorder, as utilized, for example, in assessing the content of disorder in proteomes.  ...  However, the prediction accuracy of disordered predictors is not calibrated, nor is it established whether predictors are intrinsically biased towards one of the extremes of the order-disorder axis.  ...  Kozlowski for help with batch submissions on the genesilico server.  ... 
doi:10.1038/s41598-019-41644-w pmid:30914747 pmcid:PMC6435736 fatcat:ejqvsfal6rhxthqukejz7yl7xq

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

Lukasz P Kozlowski, Janusz M Bujnicki
2012 BMC Bioinformatics  
As of December 2011, approximately 60 methods for computational prediction of protein disorder from sequence have been made publicly available.  ...  The discovery of IUPs challenged the traditional protein structure paradigm, which stated that a specific well-defined structure defines the function of the protein.  ...  LPK was supported by the Polish Ministry of Science and Higher Education (grant NN301 190139).  ... 
doi:10.1186/1471-2105-13-111 pmid:22624656 pmcid:PMC3465245 fatcat:6ywc42vs7nc3nhak6lwxrk4oa4

Comprehensive large-scale assessment of intrinsic protein disorder

Ian Walsh, Manuel Giollo, Tomás Di Domenico, Carlo Ferrari, Olav Zimmermann, Silvio C. E. Tosatto
2014 Computer applications in the biosciences : CABIOS  
Motivation: Intrinsically disordered regions are key for the function of numerous proteins.  ...  In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations.  ...  ACKNOWLEDGEMENT The authors are grateful to members of the BioComputing UP lab for insightful discussions. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu625 pmid:25246432 fatcat:jnrbww3nrrfjrobfw6nqhamo3a

Compositional Bias of Intrinsically Disordered Proteins and Regions and Their Predictions

Bi Zhao, Lukasz Kurgan
2022 Biomolecules  
We analyze compositional biases across four classes of disorder: fully disordered proteins; short IDRs; long IDRs; and binding IDRs.  ...  We identify three distinct biases: for the fully disordered proteins, the short IDRs and the long and binding IDRs combined.  ...  drive and dedication to popularize the studies of intrinsic disorder.  ... 
doi:10.3390/biom12070888 pmid:35883444 pmcid:PMC9313023 fatcat:qbvx7kx3yvgwxa4hssjrhp3fgy

Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins

Barbara Kalinowska, Mateusz Banach, Leszek Konieczny, Irena Roterman
2015 Entropy  
Additionally, the structure of disordered fragments which are present in jumonji proteins (as confirmed by the DisProt database) is explained on the grounds of the hydrophobic core model, suggesting that  ...  The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins belonging to the jumonji group-JARID2, JARID1A  ...  This research was supported by the Jagiellonian University Medical College grant No. K/ZDS/001531.  ... 
doi:10.3390/e17031477 fatcat:jttn5hmqrzc75h3kidxydcny2q

HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences [article]

Tristan Bitard-Feildel, Isabelle Callebaut
2018 bioRxiv   pre-print
fast diverging proteins or domains with intrinsically disordered regions.  ...  The developed tools can be either used from command line or from a python API. Availability: HCAtk and pyHCA are available at https://github.com/T-B-F/pyHCA under the CeCILL-C license.  ...  The HCA p-value assessing the globularity of delineated foldable segment, is computed using the empirical distribution from DisProt sequences.  ... 
doi:10.1101/249995 fatcat:546ly6bw35ccdnsye3iqmmgnb4

How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe

Philippe Lieutaud, François Ferron, Alexey V. Uversky, Lukasz Kurgan, Vladimir N. Uversky, Sonia Longhi
2016 Intrinsically Disordered Proteins  
This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved  ...  In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered.  ...  The compositional profile of typical intrinsically disordered proteins from the DisProt database is shown for comparison (B). Figure 3 . 3 HCA plot of human prothymosin a (UniProt ID: P06454).  ... 
doi:10.1080/21690707.2016.1259708 pmid:28232901 pmcid:PMC5314888 fatcat:zetixzpkyvhntjv4pkwmrfu5ee
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