FKRR-MVSF: A Fuzzy Kernel Ridge Regression Model for Identifying DNA-Binding Proteins by Multi-View Sequence Features via Chou’s Five-Step Rule

Advance in predicting subcellular localization of multi-label proteins and its implication for developing multi-target drugs

(2019) Kuo-Chen Chou   CURRENT MEDICINAL CHEMISTRY

Incorporating Distance-based Top-n-gram and Random Forest to Identify Electron Transport Proteins

(2019) Xiaoqing Ru et al.   JOURNAL OF PROTEOME RESEARCH

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

Progresses in Predicting Post-translational Modification

(2019) Kuo-Chen Chou   International Journal of Peptide Research and Therapeutics

dForml(KNN)-PseAAC: Detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou's 5-step rule and pseudo components

(2019) Qiao Ning et al.   JOURNAL OF THEORETICAL BIOLOGY

Prediction of Potential Disease-Associated MicroRNAs by Using Neural Networks

(2019) Xiangxiang Zeng et al.   Molecular Therapy-Nucleic Acids

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

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique

(2018) Cangzhi Jia et al.   BIOINFORMATICS

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

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

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

(2018) Leyi Wei et al.   BIOINFORMATICS

A Model Stacking Framework for Identifying DNA Binding Proteins by Orchestrating Multi-View Features and Classifiers

(2018) Xiu-Juan Liu et al.   Genes

Effective DNA binding protein prediction by using key features via Chou’s general PseAAC

(2018) Sheikh Adilina et al.   JOURNAL OF THEORETICAL BIOLOGY

Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

(2018) Quan Zou et al.   RNA

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

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information

(2017) Leyi Wei et al.   INFORMATION SCIENCES

Predicting protein-protein interactions via multivariate mutual information of protein sequences

(2016) Yijie Ding et al.   BMC BIOINFORMATICS

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

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

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

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

(2015) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

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

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

(2015) Ruifeng Xu et al.   BMC Systems Biology

iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach

(2015) Xuan Xiao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

iPPI-Esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC

(2015) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

(2015) Wei Chen et al.   Molecular BioSystems

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation

(2015) Bin Liu et al.   Scientific Reports

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Prediction of protein-protein interactions from amino acid sequences using a novel multi-scale continuous and discontinuous feature set

(2014) Zhu-Hong You et al.   BMC BIOINFORMATICS

PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation

(2014) Bin Liu et al.   Molecular Informatics

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Naïve Bayes

(2014) Wangchao Lou et al.   PLoS One

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

(2014) Bin Liu et al.   PLoS One

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition

(2013) Yan Xu et al.   PLoS One

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

DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest

(2012) K. Krishna. Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

(2011) Wei-Zhong Lin et al.   PLoS One

iDBPs: a web server for the identification of DNA binding proteins

(2010) Guy Nimrod et al.   BIOINFORMATICS

On Position-Specific Scoring Matrix for Protein Function Prediction

(2010) Jong Cheol Jeong et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology

(2009) Kuo-Chen Chou   Current Proteomics