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

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

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

Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features

(2014) Qurrat U. Ain et al.   Integrative Biology

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

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

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

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

iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition

(2013) Yan Xu et al.   PLoS One

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

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

Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets

(2013) Gerard JP van Westen et al.   Journal of Cheminformatics

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

(2013) Gerard JP van Westen 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

Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data

(2012) Gerard J. P. van Westen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development

(2011) Gerard J. P. van Westen et al.   PLoS One

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

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

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

PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition

(2007) Hong-Bin Shen et al.   ANALYTICAL BIOCHEMISTRY