Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate

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

pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC

(2017) Xiang Cheng et al.   GENE

iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier

(2017) Wang-Ren Qiu et al.   GENOMICS

Predict protein structural class by incorporating two different modes of evolutionary information into Chou's general pseudo amino acid composition

(2017) Yunyun Liang et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou’s PseAAC

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

CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake Efficiency

(2017) Leyi Wei et al.   JOURNAL OF PROTEOME RESEARCH

OOgenesis_Pred: A sequence-based method for predicting oogenesis proteins by six different modes of Chou's pseudo amino acid composition

(2017) Maryam Rahimi et al.   JOURNAL OF THEORETICAL BIOLOGY

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

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

pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC

(2017) Xiang Cheng et al.   Molecular BioSystems

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

HPSLPred: An Ensemble Multi-Label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source

(2017) Shixiang Wan et al.   PROTEOMICS

Prediction of the aquatic toxicity of aromatic compounds to tetrahymena pyriformis through support vector regression

(2017) Qiang Su et al.   Oncotarget

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

(2017) Wang-Ren Qiu et al.   Oncotarget

iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features

(2017) Shahana Yasmin Chowdhury et al.   Scientific Reports

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

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

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

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

iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework

(2016) Bin Liu et al.   BIOINFORMATICS

Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features

(2016) Ming-an Sun et al.   BMC BIOINFORMATICS

Detecting false positive sequence homology: a machine learning approach

(2016) M. Stanley Fujimoto et al.   BMC BIOINFORMATICS

Protein Folds Prediction with Hierarchical Structured SVM

(2016) Dapeng Li et al.   Current Proteomics

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

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

(2016) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

(2016) Ying Hong Li et al.   PLoS One

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

(2016) Wei Chen 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

Prediction of donor splice sites using random forest with a new sequence encoding approach

(2016) Prabina Kumar Meher et al.   BioData Mining

Comparison of FDA Approved Kinase Targets to Clinical Trial Ones: Insights from Their System Profiles and Drug-Target Interaction Networks

(2016) Jingyu Xu et al.   Biomed Research International

The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective

(2016) Ying Hong Li et al.   PLoS One

Exploring the Inhibitory Mechanism of Approved Selective Norepinephrine Reuptake Inhibitors and Reboxetine Enantiomers by Molecular Dynamics Study

(2016) Guoxun Zheng et al.   Scientific Reports

Improving classification of mature microRNA by solving class imbalance problem

(2016) Ying Wang et al.   Scientific Reports

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

(2016) Bo Li et al.   Scientific Reports

Identification of dual active agents targeting 5-HT1A and SERT by combinatorial virtual screening methods

(2015) Panpan Wang et al.   BIO-MEDICAL MATERIALS AND ENGINEERING

Integrated web visualizations for protein-protein interaction databases

(2015) Fleur Jeanquartier et al.   BMC BIOINFORMATICS

Discrimination of acidic and alkaline enzyme using Chou’s pseudo amino acid composition in conjunction with probabilistic neural network model

(2015) Zaheer Ullah Khan et al.   JOURNAL OF THEORETICAL BIOLOGY

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

Targeting mitochondria metabolism for cancer therapy

(2015) Samuel E Weinberg et al.   Nature Chemical Biology

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

CATH FunFHMMer web server: protein functional annotations using functional family assignments

(2015) Sayoni Das et al.   NUCLEIC ACIDS RESEARCH

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity

(2015) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

SIFTER search: a web server for accurate phylogeny-based protein function prediction

(2015) Sayed M. Sahraeian et al.   NUCLEIC ACIDS RESEARCH

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A review ofin silicoapproaches for analysis and prediction of HIV-1-human protein–protein interactions

(2014) Sanghamitra Bandyopadhyay et al.   BRIEFINGS IN BIOINFORMATICS

In silico prediction of physical protein interactions and characterization of interactome orphans

(2014) Max Kotlyar et al.   NATURE METHODS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Some remarks on predicting multi-label attributes in molecular biosystems

(2013) Kuo-Chen Chou   Molecular BioSystems

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

An Artificial Functional Family Filter in Homolog Searching in Next-generation Sequencing Metagenomics

(2013) Ruofei Du 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

Is EC class predictable from reaction mechanism?

(2012) Neetika Nath et al.   BMC BIOINFORMATICS

CombFunc: predicting protein function using heterogeneous data sources

(2012) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Drug Discovery Prospect from Untapped Species: Indications from Approved Natural Product Drugs

(2012) Feng Zhu et al.   PLoS One

An RNA virus hijacks an incognito function of a DNA repair enzyme

(2012) R. Virgen-Slane et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GPCR-MPredictor: multi-level prediction of G protein-coupled receptors using genetic ensemble

(2011) Muhammad Naveed et al.   AMINO ACIDS

Protein function prediction: towards integration of similarity metrics

(2011) Serkan Erdin et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting

(2011) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating computational protein function prediction into drug discovery initiatives

(2010) Marianne A. Grant   DRUG DEVELOPMENT RESEARCH

Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition

(2010) Maqsood Hayat 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

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Trends in the Exploration of Anticancer Targets and Strategies in Enhancing the Efficacy of Drug Targeting

(2010) F. Zhu et al.   Current Molecular Pharmacology

ESG: extended similarity group method for automated protein function prediction

(2009) Meghana Chitale et al.   BIOINFORMATICS

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

(2009) JB Brown et al.   BMC BIOINFORMATICS

What Are Next Generation Innovative Therapeutic Targets? Clues from Genetic, Structural, Physicochemical, and Systems Profiles of Successful Targets

(2009) F. Zhu et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines

(2008) Y. Chen et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

FFPred: an integrated feature-based function prediction server for vertebrate proteomes

(2008) A. E. Lobley et al.   NUCLEIC ACIDS RESEARCH

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH