Literature DB >> 28369666

Computational Prediction of Intrinsic Disorder in Proteins.

Fanchi Meng1, Vladimir Uversky2,3, Lukasz Kurgan4.   

Abstract

Computational prediction of intrinsically disordered proteins (IDPs) is a mature research field. These methods predict disordered residues and regions in an input protein chain. More than 60 predictors of IDPs have been developed. This unit defines computational prediction of intrinsic disorder, summarizes major types of predictors of disorder, and provides details about three accurate and recently released methods. We demonstrate the use of these methods to predict intrinsic disorder for several illustrative proteins, provide insights into how predictions should be interpreted, and quantify and discuss predictive performance. Predictions can be freely and conveniently obtained using webservers. We point to the availability of databases that provide access to annotations of intrinsic disorder determined by structural studies and putative intrinsic disorder pre-computed by computational methods. Lastly, we also summarize experimental methods that can be used to validate computational predictions. © 2017 by John Wiley & Sons, Inc.
Copyright © 2017 John Wiley & Sons, Inc.

Entities:  

Keywords:  intrinsic disorder; intrinsically disordered protein; prediction

Mesh:

Substances:

Year:  2017        PMID: 28369666     DOI: 10.1002/cpps.28

Source DB:  PubMed          Journal:  Curr Protoc Protein Sci        ISSN: 1934-3655


  11 in total

1.  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

2.  Granulins modulate liquid-liquid phase separation and aggregation of the prion-like C-terminal domain of the neurodegeneration-associated protein TDP-43.

Authors:  Anukool A Bhopatkar; Vladimir N Uversky; Vijayaraghavan Rangachari
Journal:  J Biol Chem       Date:  2020-01-06       Impact factor: 5.157

3.  On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins.

Authors:  Michael Vincent; Vladimir N Uversky; Santiago Schnell
Journal:  Proteomics       Date:  2019-03-01       Impact factor: 3.984

4.  Complementarity of the residue-level protein function and structure predictions in human proteins.

Authors:  Bálint Biró; Bi Zhao; Lukasz Kurgan
Journal:  Comput Struct Biotechnol J       Date:  2022-05-06       Impact factor: 6.155

5.  Evolution of Protein Ductility in Duplicated Genes of Plants.

Authors:  Inmaculada Yruela; Bruno Contreras-Moreira; A Keith Dunker; Karl J Niklas
Journal:  Front Plant Sci       Date:  2018-08-20       Impact factor: 5.753

6.  Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins.

Authors:  Sina Ghadermarzi; Xingyi Li; Min Li; Lukasz Kurgan
Journal:  Front Genet       Date:  2019-11-15       Impact factor: 4.599

Review 7.  Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins.

Authors:  Akila Katuwawala; Lukasz Kurgan
Journal:  Biomolecules       Date:  2020-12-04

8.  A unique view of SARS-CoV-2 through the lens of ORF8 protein.

Authors:  Sk Sarif Hassan; Alaa A A Aljabali; Pritam Kumar Panda; Shinjini Ghosh; Diksha Attrish; Pabitra Pal Choudhury; Murat Seyran; Damiano Pizzol; Parise Adadi; Tarek Mohamed Abd El-Aziz; Antonio Soares; Ramesh Kandimalla; Kenneth Lundstrom; Amos Lal; Gajendra Kumar Azad; Vladimir N Uversky; Samendra P Sherchan; Wagner Baetas-da-Cruz; Bruce D Uhal; Nima Rezaei; Gaurav Chauhan; Debmalya Barh; Elrashdy M Redwan; Guy W Dayhoff; Nicolas G Bazan; Ángel Serrano-Aroca; Amr El-Demerdash; Yogendra K Mishra; Giorgio Palu; Kazuo Takayama; Adam M Brufsky; Murtaza M Tambuwala
Journal:  Comput Biol Med       Date:  2021-04-15       Impact factor: 6.698

Review 9.  Deep learning in prediction of intrinsic disorder in proteins.

Authors:  Bi Zhao; Lukasz Kurgan
Journal:  Comput Struct Biotechnol J       Date:  2022-03-08       Impact factor: 7.271

10.  idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R.

Authors:  William M McFadden; Judith L Yanowitz
Journal:  PLoS One       Date:  2022-04-18       Impact factor: 3.752

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