RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance

Prediction of lysine post-translational modifications using bioinformatic tools

(2014) Daniel Schwartz   Essays in Biochemistry

hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

(2013) Zhen Chen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites

(2013) Xiang Chen et al.   BIOINFORMATICS

System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress

(2013) Alex H. M. Ng et al.   MOLECULAR & CELLULAR PROTEOMICS

MobiDB: a comprehensive database of intrinsic protein disorder annotations

(2012) T. Di Domenico et al.   BIOINFORMATICS

Refined Preparation and Use of Anti-diglycine Remnant (K-ε-GG) Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments

(2012) Namrata D. Udeshi et al.   MOLECULAR & CELLULAR PROTEOMICS

Prediction of lysine ubiquitination with mRMR feature selection and analysis

(2011) Yudong Cai et al.   AMINO ACIDS

ESpritz: accurate and fast prediction of protein disorder

(2011) Ian Walsh et al.   BIOINFORMATICS

Intrinsic Disorder in Ubiquitination Substrates

(2011) Tzachi Hagai et al.   JOURNAL OF MOLECULAR BIOLOGY

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

(2011) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Deconstruction for Reconstruction: The Role of Proteolysis in Neural Plasticity and Disease

(2011) Baris Bingol et al.   NEURON

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

(2011) Zhen Chen et al.   PLoS One

Evaluation of disorder predictions in CASP9

(2011) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Nonproteolytic Functions of Ubiquitin in Cell Signaling

(2009) Zhijian J. Chen et al.   MOLECULAR CELL

Identification, analysis, and prediction of protein ubiquitination sites

(2009) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational identification of ubiquitylation sites from protein sequences

(2008) Chun-Wei Tung et al.   BMC BIOINFORMATICS

Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ Review Series

(2008) Fumiyo Ikeda et al.   EMBO REPORTS

Predicting Protein Post-translational Modifications Using Meta-analysis of Proteome Scale Data Sets

(2008) Daniel Schwartz et al.   MOLECULAR & CELLULAR PROTEOMICS