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

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

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design

(2013) A J Kooistra et al.   BRITISH JOURNAL OF PHARMACOLOGY

Comparison of Confirmed Inactive and Randomly Selected Compounds as Negative Training Examples in Support Vector Machine-Based Virtual Screening

(2013) Kathrin Heikamp et al.   Journal of Chemical Information and Modeling

A ligand's-eye view of protein similarity

(2013) Gerard J P van Westen et al.   NATURE METHODS

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

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

Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data

(2013) Gerard J. P. van Westen et al.   PLoS Computational Biology

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling

(2012) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

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

Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space

(2011) Eelke van der Horst et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

ChEMBL: a large-scale bioactivity database for drug discovery

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

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

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

A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization

(2010) Eelke van der Horst et al.   BMC BIOINFORMATICS

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Mining protein dynamics from sets of crystal structures using “consensus structures”

(2010) Gerard J. P. van Westen et al.   PROTEIN SCIENCE

Gaussian process: an alternative approach for QSAM modeling of peptides

(2009) Peng Zhou et al.   AMINO ACIDS

ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues

(2009) Li Yang et al.   AMINO ACIDS

Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates

(2009) Aleksejs Kontijevskis et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands

(2009) Nathanael Weill et al.   Journal of Chemical Information and Modeling

Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors

(2009) Maris Lapins et al.   Journal of Chemical Information and Modeling

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

(2009) Andreas Bender et al.   Journal of Chemical Information and Modeling

Interpretable Numerical Descriptors of Amino Acid Space

(2009) Alexander G. Georgiev   JOURNAL OF COMPUTATIONAL BIOLOGY

Proteochemometric modeling of HIV protease susceptibility

(2008) Maris Lapins et al.   BMC BIOINFORMATICS

Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space

(2008) Helena Strömbergsson et al.   Journal of Chemical Information and Modeling