Understanding protein non-folding

VN Uversky, AK Dunker - Biochimica et Biophysica Acta (BBA)-Proteins …, 2010 - Elsevier
This review describes the family of intrinsically disordered proteins, members of which fail to
form rigid 3-D structures under physiological conditions, either along their entire lengths or …

BIOPEP database and other programs for processing bioactive peptide sequences

P Minkiewicz, J Dziuba, A Iwaniak… - Journal of AOAC …, 2008 - academic.oup.com
This review presents the potential for application of computational tools in peptide science
based on a sample BIOPEP database and program as well as other programs and …

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

DT Jones, D Cozzetto - Bioinformatics, 2015 - academic.oup.com
Motivation: A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions
(IDRs), which act in unfolded states or by undergoing transitions between structured and …

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks

J Hanson, Y Yang, K Paliwal, Y Zhou - Bioinformatics, 2017 - academic.oup.com
Motivation Capturing long-range interactions between structural but not sequence neighbors
of proteins is a long-standing challenging problem in bioinformatics. Recently, long short …

PONDR-FIT: a meta-predictor of intrinsically disordered amino acids

B Xue, RL Dunbrack, RW Williams, AK Dunker… - … et Biophysica Acta (BBA …, 2010 - Elsevier
Protein intrinsic disorder is becoming increasingly recognized in proteomics research. While
lacking structure, many regions of disorder have been associated with biological function …

IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning

YJ Tang, YH Pang, B Liu - Bioinformatics, 2020 - academic.oup.com
Motivation Related to many important biological functions, intrinsically disordered regions
(IDRs) are widely distributed in proteins. Accurate prediction of IDRs is critical for the protein …

Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution

LJ Holt, BB Tuch, J Villén, AD Johnson, SP Gygi… - Science, 2009 - science.org
To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and
conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase …

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

LP Kozlowski, JM Bujnicki - BMC bioinformatics, 2012 - Springer
Abstract Background Intrinsically unstructured proteins (IUPs) lack a well-defined three-
dimensional structure. Some of them may assume a locally stable structure under specific …

Predicting intrinsic disorder in proteins: an overview

B He, K Wang, Y Liu, B Xue, VN Uversky, AK Dunker - Cell research, 2009 - nature.com
The discovery of intrinsically disordered proteins (IDP)(ie, biologically active proteins that do
not possess stable secondary and/or tertiary structures) came as an unexpected surprise, as …

A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction

Y Liu, X Wang, B Liu - Briefings in bioinformatics, 2019 - academic.oup.com
Intrinsically disordered proteins and regions are widely distributed in proteins, which are
associated with many biological processes and diseases. Accurate prediction of intrinsically …