MPLs-Pred: Predicting Membrane Protein-Ligand Binding Sites Using Hybrid Sequence-Based Features and Ligand-Specific Models

Deep-Resp-Forest: A deep forest model to predict anti-cancer drug response

(2019) Ran Su et al.   METHODS

Residue co-evolution helps predict interaction sites in α-helical membrane proteins

(2019) Bo Zeng et al.   JOURNAL OF STRUCTURAL BIOLOGY

A random forests quantile classifier for class imbalanced data

(2019) Robert O’Brien et al.   PATTERN RECOGNITION

Pharmacophore Mapping of ligand based virtual screening, molecular docking and molecular dynamic simulation studies for finding potent NS2B/NS3 Protease Inhibitors as potential anti-dengue drug compounds

(2018) A.Jainul Fathima et al.   Current Bioinformatics

Topology of membrane proteins — predictions, limitations and variations

(2018) Konstantinos D .Tsirigos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

HEMEsPred: Structure-Based Ligand-Specific Heme Binding Residues Prediction by Using Fast-Adaptive Ensemble Learning Scheme

(2018) Jian Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

ATPbind: Accurate Protein–ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons

(2018) Jun Hu et al.   Journal of Chemical Information and Modeling

Identification of Mammalian Enzymatic Proteins Based on Sequence-Derived Features and Species-Specific Scheme

(2018) Haiting Chai et al.   IEEE Access

Sequence clustering in bioinformatics: an empirical study

(2018) Quan Zou et al.   BRIEFINGS IN BIOINFORMATICS

A Review of DNA-binding Protein Prediction Methods

(2018) Kaiyang Qu et al.   Current Bioinformatics

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs

(2017) Jun Hu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Unb-DPC: Identify mycobacterial membrane protein types by incorporating un-biased dipeptide composition into Chou's general PseAAC

(2017) Muslim Khan et al.   JOURNAL OF THEORETICAL BIOLOGY

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

(2017) Shixiang Wan et al.   PROTEOMICS

Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm

(2016) Jian Zhang et al.   BMC BIOINFORMATICS

GPCR–drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure

(2016) Jun Hu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Accurate prediction of helix interactions and residue contacts in membrane proteins

(2016) Peter Hönigschmid et al.   JOURNAL OF STRUCTURAL BIOLOGY

Protein–protein interaction sites prediction by ensembling SVM and sample-weighted random forests

(2016) Zhi-Sen Wei et al.   NEUROCOMPUTING

Exploratory Predicting Protein Folding Model with Random Forest and Hybrid Features

(2015) Xuewei Zhao et al.   Current Proteomics

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

(2015) Konstantinos D. Tsirigos et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Li Song et al.   BMC BIOINFORMATICS

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

(2014) Jun Hu et al.   PLoS One

Structural and biophysical characterisation of membrane protein–ligand binding

(2013) Mary K. Phillips-Jones   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Membrane protein structure determination — The next generation

(2013) Isabel Moraes et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

(2013) Jianyi Yang et al.   BIOINFORMATICS

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

(2013) Pingping Sun et al.   Computational and Mathematical Methods in Medicine

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

(2013) Quan Zou et al.   Current Proteomics

Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering

(2013) Dong-Jun Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SCOP2 prototype: a new approach to protein structure mining

(2013) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

Imbalanced data classification using second-order cone programming support vector machines

(2013) Sebastián Maldonado et al.   PATTERN RECOGNITION

Protein secondary structure prediction using DWKF based on SVR-NSGAII

(2012) Mohammad Hossein Zangooei et al.   NEUROCOMPUTING

Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features

(2012) Sheng-Bao Suo et al.   PLoS One

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors

(2011) Ke Chen et al.   BIOINFORMATICS

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

(2011) Daniel B Roche et al.   BMC BIOINFORMATICS

On Position-Specific Scoring Matrix for Protein Function Prediction

(2010) Jong Cheol Jeong et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

3DLigandSite: predicting ligand-binding sites using similar structures

(2010) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin

(2009) Markus Almén et al.   BMC BIOLOGY

SITEHOUND-web: a server for ligand binding site identification in protein structures

(2009) M. Hernandez et al.   NUCLEIC ACIDS RESEARCH

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks

(2008) Angelika Fuchs et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS