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

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

The EBI RDF platform: linked open data for the life sciences

(2014) S. Jupp et al.   BIOINFORMATICS

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity

(2014) Teresa Paramo et al.   Journal of Chemical Theory and Computation

Computational chemogenomics: Is it more than inductive transfer?

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

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

myChEMBL: a virtual machine implementation of open data and cheminformatics tools

(2013) R. Ochoa et al.   BIOINFORMATICS

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

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

A historical perspective on protein crystallization from 1840 to the present day

(2013) Richard Giegé   FEBS Journal

Visually Interpretable Models of Kinase Selectivity Related Features Derived from Field-Based Proteochemometrics

(2013) Vigneshwari Subramanian et al.   Journal of Chemical Information and Modeling

Using Random Forest To Model the Domain Applicability of Another Random Forest Model

(2013) Robert P. Sheridan   Journal of Chemical Information and Modeling

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Comparability of Mixed IC50 Data – A Statistical Analysis

(2013) Tuomo Kalliokoski et al.   PLoS One

Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions

(2013) Faizan Sahigara et al.   Journal of Cheminformatics

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

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

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

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

Three Useful Dimensions for Domain Applicability in QSAR Models Using Random Forest

(2012) Robert P. Sheridan   Journal of Chemical Information and Modeling

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

A support vector machine-recursive feature elimination feature selection method based on artificial contrast variables and mutual information

(2012) Xiaohui Lin et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

The Experimental Uncertainty of Heterogeneous Public Ki Data

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

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger 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

On the origins of drug polypharmacology

(2012) Xavier Jalencas et al.   MedChemComm

Similarity methods in chemoinformatics

(2011) Peter Willett   ANNUAL REVIEW OF INFORMATION SCIENCE AND TECHNOLOGY

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

(2011) Kathleen M Doherty et al.   BMC BIOINFORMATICS

Quantitative Chemogenomics: Machine-Learning Models of Protein-Ligand Interaction

(2011) Claes R. Andersson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Chemogenomic Approaches for the Exploration of GPCR Space

(2011) Nathanael Weill   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions

(2011) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

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

Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques

(2010) Maris Lapins et al.   BMC BIOINFORMATICS

Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets

(2010) Christian Kramer et al.   Journal of Chemical Information and Modeling

Applicability domain for in silico models to achieve accuracy of experimental measurements

(2010) Iurii Sushko et al.   JOURNAL OF CHEMOMETRICS

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

Proteochemometric Modeling of the Susceptibility of Mutated Variants of the HIV-1 Virus to Reverse Transcriptase Inhibitors

(2010) Muhammad Junaid et al.   PLoS One

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

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

Computational Modeling of Kinase Inhibitor Selectivity

(2010) Govindan Subramanian et al.   ACS Medicinal Chemistry Letters

Drawing the PDB: Protein−Ligand Complexes in Two Dimensions

(2010) Katrin Stierand et al.   ACS Medicinal Chemistry Letters

Estimation of the applicability domain of kernel-based machine learning models for virtual screening

(2010) Nikolas Fechner et al.   Journal of Cheminformatics

Ligand Prediction for Orphan Targets Using Support Vector Machines and Various Target-Ligand Kernels Is Dominated by Nearest Neighbor Effects

(2009) Anne Mai Wassermann et al.   Journal of Chemical Information and Modeling

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

Proteochemometric modeling of HIV protease susceptibility

(2008) Maris Lapins et al.   BMC BIOINFORMATICS

Virtual screening of GPCRs: An in silico chemogenomics approach

(2008) Laurent Jacob et al.   BMC BIOINFORMATICS

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY