Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams

pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC

(2018) Xiang Cheng et al.   GENOMICS

PSSM-Suc: Accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction

(2017) Abdollah Dehzangi et al.   JOURNAL OF THEORETICAL BIOLOGY

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

2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function

(2017) Bin Liu 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

The world of protein acetylation

(2016) Adrian Drazic et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

iRSpot-EL: identify recombination spots with an ensemble learning approach

(2016) Bin Liu et al.   BIOINFORMATICS

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

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

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

SuccinSite: a computational tool for the prediction of protein succinylation sites by exploiting the amino acid patterns and properties

(2016) Md. Mehedi Hasan et al.   Molecular BioSystems

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

iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets

(2016) Jianhua Jia et al.   MOLECULES

iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences

(2016) Wei Chen 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

Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features

(2015) Abdollah Dehzangi et al.   BMC BIOINFORMATICS

Recent Progress in Predicting Posttranslational Modification Sites in Proteins

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

Predict Gram-Positive and Gram-Negative Subcellular Localization via Incorporating Evolutionary Information and Physicochemical Features Into Chou's General PseAAC

(2015) Ronesh Sharma et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

A mixture of physicochemical and evolutionary-based feature extraction approaches for protein fold recognition

(2015) Abdollah Dehzangi et al.   International Journal of Data Mining and Bioinformatics

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

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

(2015) Bin Liu et al.   JOURNAL OF THEORETICAL BIOLOGY

Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique

(2015) Xiaowei Zhao et al.   JOURNAL OF THEORETICAL BIOLOGY

Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou׳s general PseAAC

(2015) Abdollah Dehzangi et al.   JOURNAL OF THEORETICAL BIOLOGY

Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition

(2015) Harsh Saini et al.   JOURNAL OF THEORETICAL BIOLOGY

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation

(2015) Matthew D. Hirschey et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity

(2015) Yan Xu et al.   Scientific Reports

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

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information

(2014) Kuldip K Paliwal et al.   BMC BIOINFORMATICS

Proposing a highly accurate protein structural class predictor using segmentation-based features

(2014) Abdollah Dehzangi et al.   BMC GENOMICS

A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition

(2014) Kuldip K. Paliwal et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

A Segmentation-Based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition

(2014) Abdollah Dehzangi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

(2014) James Lyons et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evaluation of Sequence Features from Intrinsically Disordered Regions for the Estimation of Protein Function

(2014) Alok Sharma et al.   PLoS One

iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition

(2014) Yan Xu et al.   PLoS One

Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling

(2014) Frédéric Lamoliatte et al.   Nature Communications

iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels

(2014) Hui Ding et al.   Biomed Research International

A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition

(2013) Alok Sharma et al.   BMC BIOINFORMATICS

Glycated Lysine Residues: A Marker for Non-Enzymatic Protein Glycation in Age-Related Diseases

(2013) Nadeem A. Ansari et al.   DISEASE MARKERS

A Combination of Feature Extraction Methods with an Ensemble of Different Classifiers for Protein Structural Class Prediction Problem

(2013) Abdollah Dehzangi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting anticancer peptides with Chou′s pseudo amino acid composition and investigating their mutagenicity via Ames test

(2013) Zohre Hajisharifi et al.   JOURNAL OF THEORETICAL BIOLOGY

CPLM: a database of protein lysine modifications

(2013) Zexian Liu 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

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

(2013) Yan Xu et al.   PeerJ

A feature extraction technique using bi-gram probabilities of position specific scoring matrix for protein fold recognition

(2012) Alok Sharma et al.   JOURNAL OF THEORETICAL BIOLOGY

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Identification of lysine succinylation as a new post-translational modification

(2010) Zhihong Zhang et al.   Nature Chemical Biology

CPLA 1.0: an integrated database of protein lysine acetylation

(2010) Zexian Liu et al.   NUCLEIC ACIDS RESEARCH

Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms

(2008) Kuo-Chen Chou et al.   Nature Protocols