Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures

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

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

iMem-Seq: A Multi-label Learning Classifier for Predicting Membrane Proteins Types

(2015) Xuan Xiao et al.   JOURNAL OF MEMBRANE BIOLOGY

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

(2015) Bin Liu 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

Protein–protein interactions among enzymes of starch biosynthesis in high-amylose barley genotypes reveal differential roles of heteromeric enzyme complexes in the synthesis of A and B granules

(2015) Zaheer Ahmed et al.   PLANT SCIENCE

Identification of Real MicroRNA Precursors with a Pseudo Structure Status Composition Approach

(2015) Bin Liu et al.   PLoS One

iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Protein–protein binding affinity prediction from amino acid sequence

(2014) K. Yugandhar et al.   BIOINFORMATICS

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

(2014) Shou-Hui Guo et al.   BIOINFORMATICS

A New Multi-label Classifier in Identifying the Functional Types of Human Membrane Proteins

(2014) Hong-Liang Zou et al.   JOURNAL OF MEMBRANE BIOLOGY

Sequence-based prediction of protein–protein interaction sites with L1-logreg classifier

(2014) Kaustubh Dhole et al.   JOURNAL OF THEORETICAL BIOLOGY

HIV-1, human interaction database: current status and new features

(2014) Danso Ako-Adjei 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

Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

(2014) Engin Cukuroglu 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

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

(2014) Yan Xu et al.   PLoS One

A New Supervised Over-Sampling Algorithm with Application to Protein-Nucleotide Binding Residue Prediction

(2014) Jun Hu et al.   PLoS One

An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

(2014) Govindarajan Sudha et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches

(2014) K. Yugandhar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Learning protein multi-view features in complex space

(2013) Dong-Jun Yu et al.   AMINO ACIDS

iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types

(2013) Xuan Xiao et al.   ANALYTICAL BIOCHEMISTRY

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein

(2013) Neeraj J. Agrawal et al.   FEBS LETTERS

TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble

(2013) Dong-Jun Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins

(2013) Wei-Zhong Lin et al.   Molecular BioSystems

Some remarks on predicting multi-label attributes in molecular biosystems

(2013) Kuo-Chen Chou   Molecular BioSystems

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Protein Interactions in Genome Maintenance as Novel Antibacterial Targets

(2013) Aimee H. Marceau et al.   PLoS One

Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling

(2012) Dong-Jun Yu et al.   NEUROCOMPUTING

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

(2012) Ching-Tai Chen et al.   PLoS One

Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

(2011) Lele Hu et al.   PLoS One

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

(2010) Yoichi Murakami et al.   BIOINFORMATICS

ON MULTI-CLASS COST-SENSITIVE LEARNING

(2010) Zhi-Hua Zhou et al.   COMPUTATIONAL INTELLIGENCE

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Sequence-based prediction of protein interaction sites with an integrative method

(2009) Xue-wen Chen et al.   BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Boosting support vector machines for imbalanced data sets

(2009) Benjamin X. Wang et al.   KNOWLEDGE AND INFORMATION SYSTEMS

Energy based approach for understanding the recognition mechanism in protein–protein complexes

(2009) M. Michael Gromiha et al.   Molecular BioSystems

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

(2009) Mile Šikić et al.   PLoS Computational Biology

Targeting and tinkering with interaction networks

(2008) Robert B Russell et al.   Nature Chemical Biology

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PSAIA - Protein Structure and Interaction Analyzer

(2008) Josip Mihel et al.   BMC STRUCTURAL BIOLOGY