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DisProt: a database of protein disorder

S. Vucetic, Z. Obradovic, V. Vacic, P. Radivojac, K. Peng, L. M. Iakoucheva, M. S. Cortese, J. D. Lawson, C. J. Brown, J. G. Sikes, C. D. Newton, A. K. Dunker
2004 Bioinformatics  
The Database of Protein Disorder (DisProt) is a curated database that provides structure and function information about proteins that lack a fixed three-dimensional (3D) structure under putatively native  ...  Starting from the central premise that intrinsic disorder is an important structural class of protein and in order to meet the increasing interest thereof, DisProt is aimed at becoming a central repository  ...  A major hindrance in the study of intrinsically disordered proteins is the absence of an organized database for these proteins.  ... 
doi:10.1093/bioinformatics/bth476 pmid:15310560 fatcat:fn47wgshnfbzbnyf7r6rizgwxm

DisProt: the Database of Disordered Proteins

M. Sickmeier, J. A. Hamilton, T. LeGall, V. Vacic, M. S. Cortese, A. Tantos, B. Szabo, P. Tompa, J. Chen, V. N. Uversky, Z. Obradovic, A. K. Dunker
2007 Nucleic Acids Research  
The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs).  ...  In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at  ...  Oldfield, Jie Sun and Joy Nellis for their contributions to the establishment of this database.  ... 
doi:10.1093/nar/gkl893 pmid:17145717 pmcid:PMC1751543 fatcat:ekzkqkq7ubdmbawrvjqivkzltm

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

Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini (+28 others)
2016 Nucleic Acids Research  
Acids Res. (2016 doi: 10.1093/nar/gkw1056 The publishers would like to apologise for a mistake in the affiliation of one of the authors, Salvador Ventura.  ...  D1124 Nucleic Acids Research, 2017 , Vol. 45, Database issue Nucl.  ... 
doi:10.1093/nar/gkw1279 pmid:27965415 pmcid:PMC5210598 fatcat:mtgbidw4wjem7nzhwo2uyqwwte

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

Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini (+28 others)
2016 Nucleic Acids Research  
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007.  ...  for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.  ...  D220 Nucleic Acids Research, 2017, Vol. 45 , Database issue ABSTRACT The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal  ... 
doi:10.1093/nar/gkw1056 pmid:27899601 pmcid:PMC5210544 fatcat:b4frkq46bbh5tij5m45ikb5doe

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) .  ...  DisProt Proteins Residues Disorder Ordered Undefined v 7.0 756 87,494 113,712 199,724 Core 488 57,874 88,143 136,881 Complement 268 29,620 25,569 62,843 v 7.0 Virus 70 6,631 13,223  ... 
doi:10.1093/bioinformatics/btx590 pmid:28968848 fatcat:w7wrkpuqofhdpipdwsm6miesla

MobiDB: a comprehensive database of intrinsic protein disorder annotations

T. Di Domenico, I. Walsh, A. J. M. Martin, S. C. E. Tosatto
2012 Bioinformatics  
The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences.  ...  Motivation: Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role.  ...  Herein we describe MobiDB, a centralized resource for disorder annotation in protein sequences. IMPLEMENTATION MobiDB is a relational PostgreSQL database consisting of 11 tables.  ... 
doi:10.1093/bioinformatics/bts327 pmid:22661649 fatcat:gilouhjtbvbzlmv6rgvpjmahpe

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.  ...  ACKNOWLEDGEMENTS DisProt is a service of the Italian ELIXIR node. 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

DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
2017 BMC Bioinformatics  
Results: DisBind (available at http://biophy.dzu.edu.cn/DisBind) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered  ...  The database contains a total of 4232 binding residues (from UniProt and PDB structures) in which 2836 residues are in ORs and 1396 in IDRs.  ...  Funding This work was supported by the Taishan Scholars Program and Natural Science Foundation (ZR2016JL027) of Shandong province of China, National Natural Science Foundation of China (61271378, 61302186  ... 
doi:10.1186/s12859-017-1620-1 pmid:28381244 pmcid:PMC5382478 fatcat:6yftwqsebvegxevfajylpeas34

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

Tamas Lazar, Elizabeth Martínez-Pérez, Federica Quaglia, András Hatos, Lucía B Chemes, Javier A Iserte, Nicolás A Méndez, Nicolás A Garrone, Tadeo E Saldaño, Julia Marchetti, Ana Julia Velez Rueda, Pau Bernadó (+28 others)
2020 Nucleic Acids Research  
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last  ...  The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties  ...  ACKNOWLEDGEMENTS PED is maintained as a service of the ELIXIR IDP community (URL: elixir-europe.org/communities/intrinsicallydisordered-proteins).  ... 
doi:10.1093/nar/gkaa1021 pmid:33305318 pmcid:PMC7778965 fatcat:nnyx62xvknbnbbte6stad4qtn4

Computational Analysis of Position-dependent Disorder Content in DisProt Database

Jovana J. Kovačević
2012 Genomics, Proteomics & Bioinformatics  
A bioinformatics analysis of disorder content of proteins from the DisProt database has been performed with respect to position of disordered residues.  ...  A new scale of AAs has been introduced according to their disorder content in the middle part of proteins: CIFWMLYHRNVTAGQDSKEP.  ...  Acknowledgements The work presented has been financially supported by the Ministry of Education and Science, Republic of Serbia (Project No. 174021).  ... 
doi:10.1016/j.gpb.2012.01.002 pmid:22917189 pmcid:PMC5056116 fatcat:dy3poa6tjrdadozcwcocknofxm

D2P2: database of disordered protein predictions

Matt E. Oates, Pedro Romero, Takashi Ishida, Mohamed Ghalwash, Marcin J. Mizianty, Bin Xue, Zsuzsanna Dosztányi, Vladimir N. Uversky, Zoran Obradovic, Lukasz Kurgan, A. Keith Dunker, Julian Gough
2012 Nucleic Acids Research  
We present the Database of Disordered Protein Prediction (D 2 P 2 ), available at http://d2p2.pro (including website source code).  ...  An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus).  ...  ACKNOWLEDGEMENTS The authors acknowledge the efforts of all original authors for each disorder prediction method used in D 2 P 2 and their indirect contribution to the data they present.  ... 
doi:10.1093/nar/gks1226 pmid:23203878 pmcid:PMC3531159 fatcat:qs3fzoouizbexo3onedjlhmeti

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

Mihaly Varadi, Simone Kosol, Pierre Lebrun, Erica Valentini, Martin Blackledge, A. Keith Dunker, Isabella C. Felli, Julie D. Forman-Kay, Richard W. Kriwacki, Roberta Pierattelli, Joel Sussman, Dmitri I. Svergun (+5 others)
2013 Nucleic Acids Research  
The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based  ...  these data, provided as a set of models in a Protein Data Bank format.  ...  , such as DisProt (16) , the database of binary disorder classification based on biophysical data, and two sequencebased disorder databases, D 2 P 2 (17) , which holds disorder predictions, and IDEAL  ... 
doi:10.1093/nar/gkt960 pmid:24174539 pmcid:PMC3964940 fatcat:idgrucmhbfddfprti2nueuj7hq

Evaluation of Proteins with Intrinsic Disorder from the DisProt Database: Concepts, Biological Importance and Peculiar Characteristics
Avaliação de Proteínas com Desordem Intrínseca do Banco de Dados DisProt: Conceitos, Importância Biológica e Características Peculiares

Stephanny M. Alves de Souza, Theo L. F. de Souza
2022 Revista Virtual de Quimica  
The intrinsic disorder (ID) consists of a feature present in an extensive group of proteins in its totality (IDPs) or only in regions (IDRs).  ...  In this work, we perform an investigation of different issues involving proteins with ID available in the DisProt database, as well as an extensive literature search to gather information that can help  ...  em uma proteína bem enovelada, como em proteínas intrinsicamente desordenadas (IDPs, Intrinsically disordered proteins) em sua totalidade.  ... 
doi:10.21577/1984-6835.20220008 fatcat:lwdy4kat25bdbnjskewucb64qa

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, Oxana V. Galzitskaya
2009 Nucleic Acids Research  
In this work, we have created a new database (named ComSin) of protein structures in bound (complex) and unbound (single) states to provide a researcher with exhaustive information on structures of the  ...  Most of the proteins in a cell assemble into complexes to carry out their function.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp963 pmid:19906708 pmcid:PMC2808974 fatcat:asdz5crf3bgydgxzwbldcqiwre

Critical Assessment of Protein Intrinsic Disorder Prediction [article]

Marco Necci, Damiano Piovesan, Silvio C E Tosatto, CAID Predictors, DisProt Curators
2020 bioRxiv   pre-print
A total of 43 methods, 32 for disorder and 11 for binding regions, were evaluated on a dataset of 646 proteins.  ...  The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in predicting intrinsically disordered  ...  The state task "Bioinformatics and proteomics studies of proteins and their complexes" № 0115-2019-004 for OG and ML.  ... 
doi:10.1101/2020.08.11.245852 fatcat:tzys2dxya5fibghjjglpmt7p2i
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