RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest

A novel method for predicting post-translational modifications on serine and threonine sites by using site-modification network profiles

(2015) Minghui Wang et al.   Molecular BioSystems

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites

(2015) Sutapa Datta et al.   PLoS One

Predicting Protein-Protein Interactions from Primary Protein Sequences Using a Novel Multi-Scale Local Feature Representation Scheme and the Random Forest

(2015) Zhu-Hong You et al.   PLoS One

PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

(2014) Yongchao Dou et al.   AMINO ACIDS

Prediction of protein kinase-specific phosphorylation sites in hierarchical structure using functional information and random forest

(2014) Wenwen Fan et al.   AMINO ACIDS

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

(2014) Ralph Patrick et al.   BIOINFORMATICS

Improving protein fold recognition by random forest

(2014) Taeho Jo et al.   BMC BIOINFORMATICS

An ensemble method approach to investigate kinase-specific phosphorylation sites

(2014) Sutapa Datta et al.   International Journal of Nanomedicine

Toward a systems-level view of dynamic phosphorylation networks

(2014) Robert H. Newman et al.   Frontiers in Genetics

PhosphoNetworks: a database for human phosphorylation networks

(2013) J. Hu et al.   BIOINFORMATICS

Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights

(2013) B. Trost et al.   BIOINFORMATICS

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg Classifier

(2012) Yongchao Dou et al.   PLoS One

Computational prediction of eukaryotic phosphorylation sites

(2011) B. Trost et al.   BIOINFORMATICS

Prediction of catalytic residues based on an overlapping amino acid classification

(2010) Yongchao Dou et al.   AMINO ACIDS

Prediction of protein–RNA binding sites by a random forest method with combined features

(2010) Zhi-Ping Liu et al.   BIOINFORMATICS

Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information

(2010) Ashis Biswas et al.   BMC BIOINFORMATICS

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

A reexamination of information theory-based methods for DNA-binding site identification

(2009) Ivan Erill et al.   BMC BIOINFORMATICS

Phosphopeptide fragmentation and analysis by mass spectrometry

(2009) Paul J. Boersema et al.   JOURNAL OF MASS SPECTROMETRY

Similarity Analysis of Protein Sequences Based on the Normalized Relative-Entropy

(2008) Chun Li et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy

(2008) Yu Xue et al.   MOLECULAR & CELLULAR PROTEOMICS