IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields

CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction

(2018) Qiaozhen Meng et al.   BIOINFORMATICS

iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC

(2018) Bin Liu et al.   BIOINFORMATICS

StackDPPred: A Stacking based Prediction of DNA-binding Protein from Sequence

(2018) Avdesh Mishra et al.   BIOINFORMATICS

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

(2018) Jiangning Song et al.   BRIEFINGS IN BIOINFORMATICS

Feature Extractions for Computationally Predicting Protein Post- Translational Modifications

(2018) Guohua Huang et al.   Current Bioinformatics

Prediction of human protein subcellular localization using deep learning

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

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

(2018) Jiangning Song et al.   JOURNAL OF THEORETICAL BIOLOGY

Pupylation sites prediction with ensemble classification model

(2017) Wenzheng Bao et al.   International Journal of Data Mining and Bioinformatics

PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation

(2017) et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An improved sequence-based prediction protocol for protein-protein interactions using amino acids substitution matrix and rotation forest ensemble classifiers

(2017) Zhu-Hong You et al.   NEUROCOMPUTING

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods

(2017) Bin Liu et al.   Oncotarget

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks

(2016) Jack Hanson et al.   BIOINFORMATICS

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

(2016) Bin Liu et al.   BIOINFORMATICS

A comprehensive review and comparison of different computational methods for protein remote homology detection

(2016) Junjie Chen et al.   BRIEFINGS IN BIOINFORMATICS

A novel features ranking metric with application to scalable visual and bioinformatics data classification

(2016) Quan Zou et al.   NEUROCOMPUTING

DisProt 7.0: a major update of the database of disordered proteins

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

GlycoMine struct : a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

(2016) Fuyi Li et al.   Scientific Reports

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

(2015) Fuyi Li et al.   BIOINFORMATICS

Application of learning to rank to protein remote homology detection

(2015) Bin Liu et al.   BIOINFORMATICS

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

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

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

Comprehensive large-scale assessment of intrinsic protein disorder

(2014) Ian Walsh et al.   BIOINFORMATICS

CRF-based models of protein surfaces improve protein-protein interaction site predictions

(2014) Zhijie Dong et al.   BMC BIOINFORMATICS

SFAPS: An R package for structure/function analysis of protein sequences based on informational spectrum method

(2014) Su-Ping Deng et al.   METHODS

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

(2014) Bin Liu et al.   Molecular Informatics

MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins

(2014) Emilio Potenza et al.   NUCLEIC ACIDS RESEARCH

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

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

(2013) Bin Liu et al.   BIOINFORMATICS

Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso

(2013) Morihiro Hayashida et al.   BMC Systems Biology

BinMemPredict: a Web Server and Software for Predicting Membrane Protein Types

(2013) Quan Zou et al.   Current Proteomics

Assessment of protein disorder region predictions in CASP10

(2013) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MobiDB: a comprehensive database of intrinsic protein disorder annotations

(2012) T. Di Domenico et al.   BIOINFORMATICS

Comprehensive Comparative Assessment of In-Silico Predictors of Disordered Regions

(2012) Zhen-Ling Peng et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

(2012) Tuo Zhang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

ESpritz: accurate and fast prediction of protein disorder

(2011) Ian Walsh et al.   BIOINFORMATICS

Conditional random field approach to prediction of protein-protein interactions using domain information

(2011) Morihiro Hayashida et al.   BMC Systems Biology

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

(2010) Bin Xue et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

(2010) Marcin J. Mizianty et al.   BIOINFORMATICS

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

(2010) Pieter Meysman et al.   NUCLEIC ACIDS RESEARCH

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

(2009) Bin Liu et al.   BMC BIOINFORMATICS

Improved Disorder Prediction by Combination of Orthogonal Approaches

(2009) Avner Schlessinger et al.   PLoS One

Prediction of kinase-specific phosphorylation sites using conditional random fields

(2008) Thanh Hai Dang et al.   BIOINFORMATICS

Accurate sequence-based prediction of catalytic residues

(2008) Tuo Zhang et al.   BIOINFORMATICS

Intrinsic disorder prediction from the analysis of multiple protein fold recognition models

(2008) Liam J. McGuffin   BIOINFORMATICS

OnD-CRF: predicting order and disorder in proteins conditional random fields

(2008) L. Wang et al.   BIOINFORMATICS

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

(2008) Bin Liu et al.   BMC BIOINFORMATICS

Protein disorder prediction at multiple levels of sensitivity and specificity

(2008) Joshua Hecker et al.   BMC GENOMICS

A Constructive Hybrid Structure Optimization Methodology for Radial Basis Probabilistic Neural Networks

(2008) De-Shuang Huang et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS