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

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

(2015) Nan Xiao et al.   BIOINFORMATICS

Elucidating Compound Mechanism of Action by Network Perturbation Analysis

(2015) Jung Hoon Woo et al.   CELL

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

repRNA: a web server for generating various feature vectors of RNA sequences

(2015) Bin Liu et al.   MOLECULAR GENETICS AND GENOMICS

How computational models can help unlock biological systems

(2015) G. Wayne Brodland   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

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

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

STITCH 4: integration of protein–chemical interactions with user data

(2013) Michael Kuhn 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

iGPCR-Drug: A Web Server for Predicting Interaction between GPCRs and Drugs in Cellular Networking

(2013) Xuan Xiao et al.   PLoS One

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

CSB: a Python framework for structural bioinformatics

(2012) I. Kalev et al.   BIOINFORMATICS

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

(2012) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

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

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

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

Network medicine: a network-based approach to human disease

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

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

(2010) Gerard J. P. van Westen et al.   MedChemComm

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

nuScore: a web-interface for nucleosome positioning predictions

(2008) M. Y. Tolstorukov et al.   BIOINFORMATICS

BioJava: an open-source framework for bioinformatics

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

Proteochemometric modeling of HIV protease susceptibility

(2008) Maris Lapins et al.   BMC 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

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Predicting Human Nucleosome Occupancy from Primary Sequence

(2008) Shobhit Gupta et al.   PLoS Computational Biology