PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

ChemSAR: an online pipelining platform for molecular SAR modeling

(2017) Jie Dong et al.   Journal of Cheminformatics

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

(2017) José R. Valdés-Martiní et al.   Journal of Cheminformatics

Predicting human intestinal absorption with modified random forest approach: a comprehensive evaluation of molecular representation, unbalanced data, and applicability domain issues

(2017) Ning-Ning Wang et al.   RSC Advances

ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting

(2016) Ning-Ning Wang et al.   Journal of Chemical Information and Modeling

TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models

(2016) Zhi-Jiang Yao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions

(2016) Jie Dong et al.   Journal of Cheminformatics

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins

(2015) Yasser B Ruiz-Blanco et al.   BMC BIOINFORMATICS

GESSE: Predicting Drug Side Effects from Drug–Target Relationships

(2015) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

In silicoevaluation of logD7.4and comparison with other prediction methods

(2015) Jian-Bing Wang et al.   JOURNAL OF CHEMOMETRICS

ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

(2015) Jie Dong et al.   Journal of Cheminformatics

Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions

(2014) D.-S. Cao et al.   BIOINFORMATICS

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

(2014) Bin Liu 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

Applying machine learning techniques for ADME-Tox prediction: a review

(2014) Vinícius Gonçalves Maltarollo et al.   Expert Opinion on Drug Metabolism & Toxicology

QuBiLS-MIDAS: A parallel free-software for molecular descriptors computation based on multilinear algebraic maps

(2014) César R. García-Jacas et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DDI-CPI, a server that predicts drug–drug interactions through implementing the chemical–protein interactome

(2014) Heng Luo et al.   NUCLEIC ACIDS RESEARCH

Proteochemometric modeling in a Bayesian framework

(2014) Isidro Cortes-Ciriano et al.   Journal of Cheminformatics

Large-scale prediction of human kinase–inhibitor interactions using protein sequences and molecular topological structures

(2013) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Unified Multi-target Approach for the Rational in silico Design of Anti-bladder Cancer Agents

(2013) Alejandro Speck- Planche et al.   Anti-Cancer Agents in Medicinal Chemistry

ChemoPy: freely available python package for computational biology and chemoinformatics

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

Extended GT-STAF information indices based on Markov approximation models

(2013) Stephen J. Barigye et al.   CHEMICAL PHYSICS LETTERS

PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies

(2013) Dong-Sheng Cao et al.   Journal of Chemical Information and Modeling

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Screening of Drug-Target Associations Relevant to Ki Using a Chemogenomics Approach

(2013) Dong-Sheng Cao et al.   PLoS One

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

(2012) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors

(2012) Jian-Hua Huang et al.   BIOCHIMIE

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?

(2012) Alexandre Varnek et al.   Journal of Chemical Information and Modeling

ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage

(2012) Sichao Wang et al.   MOLECULAR PHARMACEUTICS

In silico classification of human maximum recommended daily dose based on modified random forest and substructure fingerprint

(2011) Dong-Sheng Cao et al.   ANALYTICA CHIMICA ACTA

Exploring nonlinear relationships in chemical data using kernel-based methods

(2011) Dong-Sheng Cao et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

CDK-Taverna: an open workflow environment for cheminformatics

(2010) Thomas Kuhn et al.   BMC BIOINFORMATICS

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

(2010) Hanna Geppert et al.   Journal of Chemical Information and Modeling

Ranking Chemical Structures for Drug Discovery: A New Machine Learning Approach

(2010) Shivani Agarwal et al.   Journal of Chemical Information and Modeling

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

(2010) Chun Wei Yap   JOURNAL OF COMPUTATIONAL CHEMISTRY

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

The boosting: A new idea of building models

(2009) Dong-Sheng Cao et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

(2008) Noel M O'Boyle et al.   Chemistry Central Journal

Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms

(2008) Kuo-Chen Chou et al.   Nature Protocols