In silico ADME/T modelling for rational drug design

Novel Bayesian classification models for predicting compounds blocking hERG potassium channels

(2014) Li-li Liu et al.   ACTA PHARMACOLOGICA SINICA

Process data analytics in the era of big data

(2014) S. Joe Qin   AICHE JOURNAL

Applicability of Computational Systems Biology in Toxicology

(2014) Kristine Kongsbak et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

(2014) Timothy S. Carpenter et al.   BIOPHYSICAL JOURNAL

Systems Toxicology: From Basic Research to Risk Assessment

(2014) Shana J. Sturla et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Electron-correlation based externally predictive QSARs for mutagenicity of nitrated-PAHs in Salmonella typhimurium TA100

(2014) Reenu et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Blood–brain barrier models and their relevance for a successful development of CNS drug delivery systems: A review

(2014) Joana Bicker et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

Data-intensive applications, challenges, techniques and technologies: A survey on Big Data

(2014) C.L. Philip Chen et al.   INFORMATION SCIENCES

Metabolism Site Prediction Based on Xenobiotic Structural Formulas and PASS Prediction Algorithm

(2014) Anastasia V. Rudik et al.   Journal of Chemical Information and Modeling

In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods

(2014) Xiao Li et al.   Journal of Chemical Information and Modeling

Acidic and Basic Drugs in Medicinal Chemistry: A Perspective

(2014) Paul S. Charifson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Systems Biology Brings New Dimensions for Structure-Based Drug Design

(2014) Jianfeng Pei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

2013 FDA drug approvals

(2014) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

ProTox: a web server for the in silico prediction of rodent oral toxicity

(2014) Malgorzata N. Drwal et al.   NUCLEIC ACIDS RESEARCH

Lean Big Data integration in systems biology and systems pharmacology

(2014) Avi Ma’ayan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Estimation of acute oral toxicity in rat using local lazy learning

(2014) Jing Lu et al.   Journal of Cheminformatics

Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers

(2014) Jonathan D Tyzack et al.   Journal of Cheminformatics

In silico site of metabolism prediction for human UGT-catalyzed reactions

(2013) Jianlong Peng et al.   BIOINFORMATICS

Synthesis and structure–activity relationships of new carbonyl guanidine derivatives as novel dual 5-HT2B and 5-HT7 receptor antagonists

(2013) Ayako Moritomo et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Systems Pharmacology for Drug Discovery and Development: Paradigm Shift or Flash in the Pan?

(2013) P Vicini et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Recent Developments in Computational Prediction of hERG Blockage

(2013) Sichao Wang et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

In Silico ADMET Prediction: Recent Advances, Current Challenges and Future Trends

(2013) Feixiong Cheng et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Considering the impact drug-like properties have on the chance of success

(2013) Iskander Yusof et al.   DRUG DISCOVERY TODAY

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

(2013) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Data-driven medicinal chemistry in the era of big data

(2013) Scott J. Lusher et al.   DRUG DISCOVERY TODAY

Improving the prediction of drug disposition in the brain

(2013) Kiril Lanevskij et al.   Expert Opinion on Drug Metabolism & Toxicology

Automated Ligand- and Structure-Based Protocol for in Silico Prediction of Human Serum Albumin Binding

(2013) Michelle Lynn Hall et al.   Journal of Chemical Information and Modeling

Pre-processing Feature Selection for Improved C&RT Models for Oral Absorption

(2013) Danielle Newby et al.   Journal of Chemical Information and Modeling

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules

(2013) Alessandro Lusci et al.   Journal of Chemical Information and Modeling

FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes

(2013) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

Contributions of Molecular Properties to Drug Promiscuity

(2013) Ákos Tarcsay et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structural Basis and SAR for G007-LK, a Lead Stage 1,2,4-Triazole Based Specific Tankyrase 1/2 Inhibitor

(2013) Andrew Voronkov et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Utility of Modeling and Simulation in Drug Development and Regulatory Review

(2013) Shiew-Mei Huang et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Combinatorial Pharmacophore Modeling of Organic Cation Transporter 2 (OCT2) Inhibitors: Insights into Multiple Inhibitory Mechanisms

(2013) Yuan Xu et al.   MOLECULAR PHARMACEUTICS

Computational methods for drug design and discovery: focus on China

(2013) Mingyue Zheng et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Identification of drug metabolites in human plasma or serum integrating metabolite prediction, LC–HRMS and untargeted data processing

(2013) Peter L Jacobs et al.   Bioanalysis

Predicting pK a values from EEM atomic charges

(2013) Radka Svobodová Vařeková et al.   Journal of Cheminformatics

Computational drug discovery

(2012) Si-sheng Ou-Yang et al.   ACTA PHARMACOLOGICA SINICA

The Future of Peptide-based Drugs

(2012) David J. Craik et al.   Chemical Biology & Drug Design

The significance of acid/base properties in drug discovery

(2012) David T. Manallack et al.   CHEMICAL SOCIETY REVIEWS

The Role of Physiologically Based Pharmacokinetic Modeling in Regulatory Review

(2012) S-M Huang et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Best Practice in the Use of Physiologically Based Pharmacokinetic Modeling and Simulation to Address Clinical Pharmacology Regulatory Questions

(2012) P Zhao et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Computer-Aided Drug Design: Lead Discovery and Optimization

(2012) Mingli Xiang et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Drug discovery in pharmaceutical industry: productivity challenges and trends

(2012) Ish Khanna   DRUG DISCOVERY TODAY

Mixture Toxicity Revisited from a Toxicogenomic Perspective

(2012) Rolf Altenburger et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The influence of lipophilicity in drug discovery and design

(2012) John A Arnott et al.   Expert Opinion on Drug Discovery

Strategies for the generation, validation and application ofin silicoADMET models in lead generation and optimization

(2012) Matthew Paul Gleeson et al.   Expert Opinion on Drug Metabolism & Toxicology

A Bayesian Approach to in Silico Blood-Brain Barrier Penetration Modeling

(2012) Ines Filipa Martins et al.   Journal of Chemical Information and Modeling

In Silico Prediction of Aqueous Solubility Using Simple QSPR Models: The Importance of Phenol and Phenol-like Moieties

(2012) Jogoth Ali et al.   Journal of Chemical Information and Modeling

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

(2012) Iurii Sushko et al.   Journal of Chemical Information and Modeling

In silico Prediction of Chemical Ames Mutagenicity

(2012) Congying Xu et al.   Journal of Chemical Information and Modeling

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

(2012) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

(2012) David S. Palmer et al.   Journal of Chemical Theory and Computation

The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field

(2012) Michael J. Schnieders et al.   Journal of Chemical Theory and Computation

Evaluation of Exposure Change of Nonrenally Eliminated Drugs in Patients With Chronic Kidney Disease Using Physiologically Based Pharmacokinetic Modeling and Simulation

(2012) Ping Zhao et al.   JOURNAL OF CLINICAL PHARMACOLOGY

Discovery of Potent, Selective Multidrug and Toxin Extrusion Transporter 1 (MATE1, SLC47A1) Inhibitors Through Prescription Drug Profiling and Computational Modeling

(2012) Matthias B. Wittwer et al.   JOURNAL OF MEDICINAL CHEMISTRY

ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage

(2012) Sichao Wang et al.   MOLECULAR PHARMACEUTICS

Quantifying the chemical beauty of drugs

(2012) G. Richard Bickerton et al.   Nature Chemistry

The Comparative Toxicogenomics Database: update 2013

(2012) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: Results from the European Project ACuteTox

(2012) P. Prieto et al.   TOXICOLOGY IN VITRO

Evaluation of drug–human serum albumin binding interactions with support vector machine aided online automated docking

(2011) Ferenc Zsila et al.   BIOINFORMATICS

Predicting human plasma protein binding of drugs using plasma protein interaction QSAR analysis (PPI-QSAR)

(2011) Haiyan Li et al.   BIOPHARMACEUTICS & DRUG DISPOSITION

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

New Uses for Old Drugs: Pharmacophore-Based Screening for the Discovery of P-Glycoprotein Inhibitors

(2011) Andreia Palmeira et al.   Chemical Biology & Drug Design

Predicting the pKa of Small Molecules

(2011) Matthias Rupp et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

A prediction model of substrates and non-substrates of breast cancer resistance protein (BCRP) developed by GA–CG–SVM method

(2011) Lei Zhong et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Structure-based drug design to augment hit discovery

(2011) Subha Kalyaanamoorthy et al.   DRUG DISCOVERY TODAY

Toward in silico structure-based ADMET prediction in drug discovery

(2011) Gautier Moroy et al.   DRUG DISCOVERY TODAY

Maximizing the outcome of early ADMET models: strategies to win the drug-hunting battles?

(2011) Jianling Wang et al.   Expert Opinion on Drug Metabolism & Toxicology

Revisiting the General Solubility Equation: In Silico Prediction of Aqueous Solubility Incorporating the Effect of Topographical Polar Surface Area

(2011) Jogoth Ali et al.   Journal of Chemical Information and Modeling

IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism

(2011) Jianing Li et al.   Journal of Chemical Theory and Computation

Profiling of a Prescription Drug Library for Potential Renal Drug–Drug Interactions Mediated by the Organic Cation Transporter 2

(2011) Yasuto Kido et al.   JOURNAL OF MEDICINAL CHEMISTRY

QSAR Analysis of Blood–Brain Distribution: The Influence of Plasma and Brain Tissue Binding

(2011) Kiril Lanevskij et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

ChEMBL: a large-scale bioactivity database for drug discovery

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

Structure–activity relationships of flavonoids as inhibitors of breast cancer resistance protein (BCRP)

(2010) Anne Pick et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Applications of Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulation During Regulatory Review

(2010) P Zhao et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection

(2010) Jian J. Tan et al.   DRUG DISCOVERY TODAY

Lipophilicity in drug discovery

(2010) Michael J Waring   Expert Opinion on Drug Discovery

Assessment ofin silicomodels for fraction of unbound drug in human liver microsomes

(2010) Hua Gao et al.   Expert Opinion on Drug Metabolism & Toxicology

Evaluation of pKaEstimation Methods on 211 Druglike Compounds

(2010) John Manchester et al.   Journal of Chemical Information and Modeling

Estimation of ADME Properties with Substructure Pattern Recognition

(2010) Jie Shen et al.   Journal of Chemical Information and Modeling

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction

(2010) David S Palmer et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Estimation of Acid Dissociation Constants Using Graph Kernels

(2010) Matthias Rupp et al.   Molecular Informatics

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

Application of toxicogenomics in hepatic systems toxicology for risk assessment: Acetaminophen as a case study

(2010) Anne S. Kienhuis et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

(2010) Patrik Rydberg et al.   ACS Medicinal Chemistry Letters

Mechanistic Approaches to Predicting Oral Drug Absorption

(2009) Weili Huang et al.   AAPS Journal

Site of metabolism prediction for six biotransformations mediated by cytochromes P450

(2009) M. Zheng et al.   BIOINFORMATICS

Quantitative Structure−Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

(2009) Hao Zhu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Physicochemical drug properties associated within vivotoxicological outcomes: a review

(2009) David A Price et al.   Expert Opinion on Drug Metabolism & Toxicology

Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas

(2009) Junmei Wang et al.   Journal of Chemical Information and Modeling

In SilicoPrediction of Aqueous Solubility: The Solubility Challenge

(2009) M. Hewitt et al.   Journal of Chemical Information and Modeling

Comparison of Nine Programs Predicting pKaValues of Pharmaceutical Substances

(2009) Chenzhong Liao et al.   Journal of Chemical Information and Modeling

1-Octanol/Water Partition Coefficients ofn-Alkanes from Molecular Simulations of Absolute Solvation Free Energies

(2009) Nuno M. Garrido et al.   Journal of Chemical Theory and Computation

Predictive Models for Carcinogenicity and Mutagenicity: Frameworks, State-of-the-Art, and Perspectives

(2009) E. BENFENATI et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART C-ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS

The Japanese toxicogenomics project: Application of toxicogenomics

(2009) Takeki Uehara et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Toxicology for the twenty-first century

(2009) Thomas Hartung   NATURE

The acid–base profile of a contemporary set of drugs: implications for drug discovery

(2009) D.T. Manallack   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

A universal approach for continuum solvent pK a calculations: are we there yet?

(2009) Junming Ho et al.   THEORETICAL CHEMISTRY ACCOUNTS

Accurate In Silico log PPredictions: One Can't Embrace the Unembraceable

(2009) Igor V. Tetko et al.   Quantitative structure-activity relationships & combinatorial science

Physiochemical drug properties associated with in vivo toxicological outcomes

(2008) Jason D. Hughes et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites

(2008) Lars Ridder et al.   ChemMedChem

Computational toxicology in drug development

(2008) Wolfgang Muster et al.   DRUG DISCOVERY TODAY

Whole body physiologically-based pharmacokinetic models: their use in clinical drug development

(2008) Andrea N Edginton et al.   Expert Opinion on Drug Metabolism & Toxicology

New Combined Model for the Prediction of Regioselectivity in Cytochrome P450/3A4 Mediated Metabolism

(2008) Won Seok Oh et al.   Journal of Chemical Information and Modeling

Solubility Challenge: Can You Predict Solubilities of 32 Molecules Using a Database of 100 Reliable Measurements?

(2008) Antonio Llinàs et al.   Journal of Chemical Information and Modeling

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

(2008) Zuzana Jiroušková et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulation Modelling of Human Intestinal Absorption using Caco-2 Permeability and Kinetic Solubility Data for Early Drug Discovery

(2008) Simon Thomas et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds

(2008) Raimund Mannhold et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Structural determinants of inhibitor interaction with the human organic cation transporter OCT2 (SLC22A2)

(2008) Oliver Zolk et al.   NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA