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

A novel machine learning method for cytokine-receptor interaction prediction

(2016) Leyi Wei et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique

(2016) Hua Tang et al.   Molecular BioSystems

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

Application of learning to rank to protein remote homology detection

(2015) Bin Liu et al.   BIOINFORMATICS

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

(2015) Ruifeng Xu et al.   BMC Systems Biology

Enhanced Protein Fold Prediction Method Through a Novel Feature Extraction Technique

(2015) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

An Improved Protein Structural Classes Prediction Method by Incorporating Both Sequence and Structure Information

(2015) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Imbalanced Protein Data Classification Using Ensemble FTM-SVM

(2015) Hong-Liang Dai   IEEE TRANSACTIONS ON NANOBIOSCIENCE

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and 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

Targeting mitochondria metabolism for cancer therapy

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

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

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

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

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

(2015) Bin Liu et al.   Scientific Reports

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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

(2014) Li Song et al.   BMC BIOINFORMATICS

Prediction of human breast and colon cancers from imbalanced data using nearest neighbor and support vector machines

(2014) Abdul Majid et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

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

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

(2014) Max Kotlyar et al.   NATURE METHODS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

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

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

(2013) Bin Liu et al.   BIOINFORMATICS

Protein function prediction using domain families

(2013) Robert Rentzsch et al.   BMC BIOINFORMATICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

LibD3C: Ensemble classifiers with a clustering and dynamic selection strategy

(2013) Chen Lin et al.   NEUROCOMPUTING

BLAST: a more efficient report with usability improvements

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier

(2013) Chen Lin et al.   PLoS One

FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences

(2013) Federico Minneci et al.   PLoS One

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

A Global Characterization and Identification of Multifunctional Enzymes

(2012) Xian-Ying Cheng et al.   PLoS One

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

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

(2011) Muhammad Naveed et al.   AMINO ACIDS

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

(2011) H. B. Rao et al.   NUCLEIC ACIDS RESEARCH

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens

(2008) Aarti Garg et al.   BMC BIOINFORMATICS

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

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

Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks

(2008) Sheila M. Reynolds et al.   PLoS Computational Biology

Predicting gene function in a hierarchical context with an ensemble of classifiers

(2008) Yuanfang Guan et al.   GENOME BIOLOGY