Proteochemometric modeling in a Bayesian framework

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Computational chemogenomics: Is it more than inductive transfer?

(2014) J. B. Brown et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Combining On-Chip Synthesis of a Focused Combinatorial Library with Computational Target Prediction Reveals Imidazopyridine GPCR Ligands

(2013) Michael Reutlinger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Design and evaluation of substrate-based octapeptide and non substrate-based tetrapeptide inhibitors of dengue virus NS2B–NS3 proteases

(2013) Peteris Prusis et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window

(2013) Alexios Koutsoukas et al.   Journal of Chemical Information and Modeling

Estimating Error Rates in Bioactivity Databases

(2013) Pekka Tiikkainen 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

Comparability of Mixed IC50 Data – A Statistical Analysis

(2013) Tuomo Kalliokoski et al.   PLoS One

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Screening of selective histone deacetylase inhibitors by proteochemometric modeling

(2012) Dingfeng Wu et al.   BMC BIOINFORMATICS

QSARs, Data and Error in the Modern Age of Drug Discovery

(2012) Christian Kramer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

The Role of Chemogenomics in the Pharmaceutical Industry

(2012) Michael Bieler et al.   DRUG DEVELOPMENT RESEARCH

Study on human GPCR–inhibitor interactions by proteochemometric modeling

(2012) Jun Gao et al.   GENE

The Experimental Uncertainty of Heterogeneous Public Ki Data

(2012) Christian Kramer et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Predicting New Indications for Approved Drugs Using a Proteochemometric Method

(2012) Sivanesan Dakshanamurthy et al.   JOURNAL OF MEDICINAL CHEMISTRY

Comparison of Different Approaches to Define the Applicability Domain of QSAR Models

(2012) Faizan Sahigara et al.   MOLECULES

Proteochemometric Modeling of the Bioactivity Spectra of HIV-1 Protease Inhibitors by Introducing Protein-Ligand Interaction Fingerprint

(2012) Qi Huang et al.   PLoS One

Global Analysis of Small Molecule Binding to Related Protein Targets

(2012) Felix A. Kruger et al.   PLoS Computational Biology

Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre

(2011) O. Spjuth et al.   BIOINFORMATICS

Characterization of the binding profile of peptide to transporter associated with antigen processing (TAP) using Gaussian process regression

(2011) Yonggang Ren et al.   COMPUTERS IN BIOLOGY AND MEDICINE

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

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

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

GPCR structure and activation: an essential role for the first extracellular loop in activating the adenosine A2B receptor

(2010) Miriam C. Peeters et al.   FASEB JOURNAL

Gaussian Processes for Classification: QSAR Modeling of ADMET and Target Activity

(2010) Olga Obrezanova et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

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

Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation

(2010) M.C. Peeters et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

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

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

Gaussian process: an alternative approach for QSAM modeling of peptides

(2009) Peng Zhou et al.   AMINO ACIDS

Healthy skepticism: assessing realistic model performance

(2009) Scott P. Brown et al.   DRUG DISCOVERY TODAY

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

Definition of the G Protein-Coupled Receptor Transmembrane Bundle Binding Pocket and Calculation of Receptor Similarities for Drug Design

(2009) David E. Gloriam et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Chemogenomics: Looking at biology through the lens of chemistry

(2009) Munikumar R. Doddareddy et al.   Statistical Analysis and Data Mining

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS

Proteochemometrics analysis of substrate interactions with dengue virus NS3 proteases

(2008) Peteris Prusis et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes

(2008) Peng Zhou et al.   BIOPOLYMERS

Proteochemometric modeling of HIV protease susceptibility

(2008) Maris Lapins et al.   BMC BIOINFORMATICS

The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist

(2008) V.-P. Jaakola et al.   SCIENCE

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology