Optimization of serine phosphorylation prediction in proteins by comparing human engineered features and deep representations

SPrenylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins

(2019) Waqar Hussain et al.   JOURNAL OF THEORETICAL BIOLOGY

Prediction of antioxidant proteins by incorporating statistical moments based features into Chou's PseAAC

(2019) Ahmad Hassan Butt et al.   JOURNAL OF THEORETICAL BIOLOGY

iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition

(2019) Muhammad Awais et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

iPhosT-PseAAC: Identify phosphothreonine sites by incorporating sequence statistical moments into PseAAC

(2018) Yaser Daanial Khan et al.   ANALYTICAL BIOCHEMISTRY

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Prediction of citrullination sites by incorporating k-spaced amino acid pairs into Chou's general pseudo amino acid composition

(2018) Zhe Ju et al.   GENE

Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC

(2018) M. Fazli Sabooh et al.   JOURNAL OF THEORETICAL BIOLOGY

iMethyl-STTNC: Identification of N 6 -methyladenosine sites by extending the Idea of SAAC into Chou's PseAAC to formulate RNA sequences

(2018) Shahid Akbar et al.   JOURNAL OF THEORETICAL BIOLOGY

iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites

(2018) Wei Chen et al.   Molecular Therapy-Nucleic Acids

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition

(2018) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Prediction Of Nitrosocysteine Sites Using Position And Composition Variant Features

(2018) Yaser Daanial Khan et al.   LETTERS IN ORGANIC CHEMISTRY

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

Capsule network for protein post-translational modification site prediction

(2018) Duolin Wang et al.   BIOINFORMATICS

NMyristoylG-PseAAC: Sequence-Based Prediction of N-Myristoyl Glycine Sites in Proteins by Integration of PseAAC and Statistical Moments

(2018) Sher Afzal Khan et al.   LETTERS IN ORGANIC CHEMISTRY

SPalmitoylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-palmitoylation sites in proteins

(2018) Waqar Hussain et al.   ANALYTICAL BIOCHEMISTRY

Prediction of lysine crotonylation sites by incorporating the composition of k -spaced amino acid pairs into Chou’s general PseAAC

(2017) Zhe Ju et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

iPGK-PseAAC: Identify Lysine Phosphoglycerylation Sites in Proteins by Incorporating Four Different Tiers of Amino Acid Pairwise Coupling Information into the General PseAAC

(2017) Li-Ming Liu et al.   Medicinal Chemistry

iRNA-2methyl: Identify RNA 2'-O-methylation Sites by Incorporating Sequence-Coupled Effects into General PseKNC and Ensemble Classifier

(2017) Wang-Ren Qiu et al.   Medicinal Chemistry

iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC

(2017) Yan Xu et al.   Medicinal Chemistry

Prediction of N-linked glycosylation sites using position relative features and statistical moments

(2017) Muhammad Aizaz Akmal et al.   PLoS One

iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition

(2017) Wang-Ren Qiu et al.   Oncotarget

Phosphorylation of the HIV-1 capsid by MELK triggers uncoating to promote viral cDNA synthesis

(2017) Hiroaki Takeuchi et al.   PLoS Pathogens

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

(2017) Pengmian Feng et al.   Molecular Therapy-Nucleic Acids

iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset

(2016) Jianhua Jia et al.   ANALYTICAL BIOCHEMISTRY

pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical–chemical properties

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

iPTM-mLys: identifying multiple lysine PTM sites and their different types

(2016) Wang-Ren Qiu et al.   BIOINFORMATICS

pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC

(2016) Jianhua Jia et al.   BIOINFORMATICS

A Treatise to Computational Approaches Towards Prediction of Membrane Protein and Its Subtypes

(2016) Ahmad Hassan Butt et al.   JOURNAL OF MEMBRANE BIOLOGY

pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach

(2016) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC

(2016) Zhe Ju et al.   JOURNAL OF THEORETICAL BIOLOGY

iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory

(2016) Wang-Ren Qiu et al.   Molecular Informatics

iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier

(2016) Wang-Ren Qiu et al.   Oncotarget

iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC

(2016) Wang-Ren Qiu et al.   Oncotarget

iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC

(2016) Jianhua Jia et al.   Oncotarget

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Recent Progress in Predicting Posttranslational Modification Sites in Proteins

(2015) Yan Xu et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Using support vector machines to identify protein phosphorylation sites in viruses

(2015) Shu-Yun Huang et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins

(2015) Kai-Yao Huang et al.   NUCLEIC ACIDS RESEARCH

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

(2015) Sean J. Humphrey et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition

(2014) Cangzhi Jia et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PSNO: Predicting Cysteine S-Nitrosylation Sites by Incorporating Various Sequence-Derived Features into the General Form of Chou’s PseAAC

(2014) Jian Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition

(2014) Yan Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model

(2014) Wang-Ren Qiu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC

(2013) H.-L. Xie et al.   PROTEIN ENGINEERING DESIGN & SELECTION

iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteineS-nitrosylation sites in proteins

(2013) Yan Xu et al.   PeerJ

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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