Literature DB >> 31870849

DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server.

Amita Barik1, Akila Katuwawala2, Jack Hanson3, Kuldip Paliwal3, Yaoqi Zhou4, Lukasz Kurgan5.   

Abstract

Computational predictions of the intrinsic disorder and its functions are instrumental to facilitate annotation for the millions of unannotated proteins. However, access to these predictors is fragmented and requires substantial effort to find them and to collect and combine their results. The DEPICTER (DisorderEd PredictIon CenTER) server provides first-of-its-kind centralized access to 10 popular disorder and disorder function predictions that cover protein and nucleic acids binding, linkers, and moonlighting regions. It automates the prediction process, runs user-selected methods on the server side, visualizes the results, and outputs all predictions in a consistent and easy-to-parse format. DEPICTER also includes two accurate consensus predictors of disorder and disordered protein binding. Empirical tests on an independent (low similarity) benchmark dataset reveal that the computational tools included in DEPICTER generate accurate predictions that are significantly better than the results secured using sequence alignment. The DEPICTER server is freely available at http://biomine.cs.vcu.edu/servers/DEPICTER/.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  intrinsically disordered proteins; intrinsically disordered region; prediction center; protein–nucleic acids interactions; webserver

Year:  2019        PMID: 31870849     DOI: 10.1016/j.jmb.2019.12.030

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  17 in total

1.  DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web.

Authors:  Maxat Kulmanov; Fernando Zhapa-Camacho; Robert Hoehndorf
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

2.  IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell.

Authors:  Bi Zhao; Akila Katuwawala; Vladimir N Uversky; Lukasz Kurgan
Journal:  Cell Mol Life Sci       Date:  2020-09-30       Impact factor: 9.261

3.  Predicting Protein Conformational Disorder and Disordered Binding Sites.

Authors:  Ketty C Tamburrini; Giulia Pesce; Juliet Nilsson; Frank Gondelaud; Andrey V Kajava; Jean-Guy Berrin; Sonia Longhi
Journal:  Methods Mol Biol       Date:  2022

4.  Targeting intrinsically disordered regions facilitates discovery of CaV3.2 inhibitory peptides for AAV-mediated peripheral analgesia.

Authors:  Seung Min Shin; Justas Lauzadis; Brandon Itson-Zoske; Yongsong Cai; Fan Fan; Gayathri Natarajan; Wai-Meng Kwok; Michelino Puopolo; Quinn H Hogan; Hongwei Yu
Journal:  Pain       Date:  2022-04-14       Impact factor: 7.926

Review 5.  Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions.

Authors:  Stefania Brocca; Rita Grandori; Sonia Longhi; Vladimir Uversky
Journal:  Int J Mol Sci       Date:  2020-11-28       Impact factor: 5.923

6.  IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation.

Authors:  Gábor Erdős; Mátyás Pajkos; Zsuzsanna Dosztányi
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

7.  flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions.

Authors:  Gang Hu; Akila Katuwawala; Kui Wang; Zhonghua Wu; Sina Ghadermarzi; Jianzhao Gao; Lukasz Kurgan
Journal:  Nat Commun       Date:  2021-07-21       Impact factor: 14.919

Review 8.  Natural Killer Lytic-Associated Molecule (NKLAM): An E3 Ubiquitin Ligase With an Integral Role in Innate Immunity.

Authors:  Donald W Lawrence; Paul A Willard; Allyson M Cochran; Emily C Matchett; Jacki Kornbluth
Journal:  Front Physiol       Date:  2020-10-29       Impact factor: 4.566

Review 9.  Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type.

Authors:  Kui Wang; Gang Hu; Zhonghua Wu; Hong Su; Jianyi Yang; Lukasz Kurgan
Journal:  Int J Mol Sci       Date:  2020-09-19       Impact factor: 5.923

10.  Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet.

Authors:  Alexandre G de Brevern
Journal:  Biomolecules       Date:  2020-07-20
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