Towards reproducible computational drug discovery

Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

(2019) Nicolas Bosc et al.   Journal of Cheminformatics

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

(2019) Fedor Kolpakov et al.   NUCLEIC ACIDS RESEARCH

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data

(2019) Dominique Sydow et al.   Journal of Cheminformatics

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

(2019) Adam Rule et al.   PLoS Computational Biology

A path to next-generation reproducibility in cheminformatics

(2019) Robert D. Clark   Journal of Cheminformatics

Enabling rootless Linux Containers in multi-user environments: The udocker tool

(2018) Jorge Gomes et al.   COMPUTER PHYSICS COMMUNICATIONS

Assessment and Reproducibility of Quantitative Structure–Activity Relationship Models by the Nonexpert

(2018) Mukesh Patel et al.   Journal of Chemical Information and Modeling

An automated framework for QSAR model building

(2018) Samina Kausar et al.   Journal of Cheminformatics

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

(2018) J. Kyle Medley et al.   PLoS Computational Biology

Tellurium: An extensible python-based modeling environment for systems and synthetic biology

(2018) Kiri Choi et al.   BIOSYSTEMS

Toward reproducible disease models using the Systems Biology Markup Language

(2018) Leandro Watanabe et al.   SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines

(2018) Neha Kulkarni et al.   BMC BIOINFORMATICS

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

(2017) Ross McGuire et al.   Journal of Chemical Information and Modeling

Platform for Unified Molecular Analysis: PUMA

(2017) Mariana González-Medina et al.   Journal of Chemical Information and Modeling

Computation semantics of the functional scientific workflow language Cuneiform

(2017) JÖRGEN BRANDT et al.   JOURNAL OF FUNCTIONAL PROGRAMMING

Software simplified

(2017) Andrew Silver   NATURE

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

ChemSAR: an online pipelining platform for molecular SAR modeling

(2017) Jie Dong et al.   Journal of Cheminformatics

Helping to improve the practice of cheminformatics

(2017) Rajarshi Guha et al.   Journal of Cheminformatics

Large-scale virtual screening on public cloud resources with Apache Spark

(2017) Marco Capuccini et al.   Journal of Cheminformatics

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

(2017) Jiangming Sun et al.   Journal of Cheminformatics

Open chemoinformatic resources to explore the structure, properties and chemical space of molecules

(2017) Mariana González-Medina et al.   RSC Advances

Ten simple rules for making research software more robust

(2017) Morgan Taschuk et al.   PLoS Computational Biology

The readability of scientific texts is decreasing over time

(2017) Pontus Plavén-Sigray et al.   eLife

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines

(2017) Baekdoo Kim et al.   GigaScience

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Drug Repositioning Through Network Pharmacology

(2016) Hao Ye et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

AutoQSAR: an automated machine learning tool for best-practice quantitative structure–activity relationship modeling

(2016) Steven L Dixon et al.   Future Medicinal Chemistry

Alarms about structural alerts

(2016) Vinicius M. Alves et al.   GREEN CHEMISTRY

Guidelines for Reproducibly Building and Simulating Systems Biology Models

(2016) J. Kyle Medley et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

(2016) Dagmar Waltemath et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

1001 Ways to run AutoDock Vina for virtual screening

(2016) Mohammad Mahdi Jaghoori et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Innovation in the pharmaceutical industry: New estimates of R&D costs

(2016) Joseph A. DiMasi et al.   JOURNAL OF HEALTH ECONOMICS

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Robust neuronal dynamics in premotor cortex during motor planning

(2016) Nuo Li et al.   NATURE

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

Biotech R&D spend jumps by more than 15%

(2016) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

DrugCentral: online drug compendium

(2016) Oleg Ursu et al.   NUCLEIC ACIDS RESEARCH

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME

(2016) Brian Drawert et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Large-scale ligand-based predictive modelling using support vector machines

(2016) Jonathan Alvarsson et al.   Journal of Cheminformatics

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

(2016) Samuel Lampa et al.   Journal of Cheminformatics

BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions

(2016) Jie Dong et al.   Journal of Cheminformatics

Tools and techniques for computational reproducibility

(2016) Stephen R. Piccolo et al.   GigaScience

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Maximizing computational tools for successful drug discovery

(2015) Chanin Nantasenamat et al.   Expert Opinion on Drug Discovery

Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application

(2015) Christophe Van Neste et al.   Forensic Science International-Genetics

Scaling Predictive Modeling in Drug Development with Cloud Computing

(2015) Behrooz Torabi Moghadam et al.   Journal of Chemical Information and Modeling

Establishing Good Computer Modelling Practice (GCMP) in the Prediction of Chemical Toxicity

(2015) Philip N. Judson et al.   Molecular Informatics

Screening Chemicals for Receptor-Mediated Toxicological and Pharmacological Endpoints: Using Public Data to Build Screening Tools within a KNIME Workflow

(2015) F. P. Steinmetz et al.   Molecular Informatics

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

A call for virtual experiments: Accelerating the scientific process

(2015) Jonathan Cooper et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Alternatives to animal testing: A review

(2015) Sonali K. Doke et al.   SAUDI PHARMACEUTICAL JOURNAL

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

(2015) George Nicola et al.   Database-The Journal of Biological Databases and Curation

RRegrs: an R package for computer-aided model selection with multiple regression models

(2015) Georgia Tsiliki et al.   Journal of Cheminformatics

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules

(2015) Daniel S Murrell et al.   Journal of Cheminformatics

QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models

(2015) V Ruusmann et al.   Journal of Cheminformatics

ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

(2015) Jie Dong et al.   Journal of Cheminformatics

The Extent and Consequences of P-Hacking in Science

(2015) Megan L. Head et al.   PLOS BIOLOGY

Ten Simple Rules for a Computational Biologist’s Laboratory Notebook

(2015) Santiago Schnell   PLoS Computational Biology

Neural coding in barrel cortex during whisker-guided locomotion

(2015) Nicholas James Sofroniew et al.   eLife

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

(2015) Janna Hastings et al.   Journal of Biomedical Semantics

Bioboxes: standardised containers for interchangeable bioinformatics software

(2015) Peter Belmann et al.   GigaScience

Virtual Reference Environments: a simple way to make research reproducible

(2014) Daniel G. Hurley et al.   BRIEFINGS IN BIOINFORMATICS

Open Innovation Drug Discovery (OIDD): A Potential Path to Novel Therapeutic Chemical Space

(2014) Maria Alvim-Gaston et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Genomic cloud computing: legal and ethical points to consider

(2014) Edward S Dove et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data

(2014) Ronald Margolis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A new open source data analysis python script for QSAR study and its validation

(2014) Vadiraj Kurdekar et al.   MEDICINAL CHEMISTRY RESEARCH

Data Mining of Chemogenomics Data Using Bi-Modal PLS Methods and Chemical Interpretation for Molecular Design

(2014) Kiyoshi Hasegawa et al.   Molecular Informatics

Research tools: Jump off the page

(2014) Amanda Mascarelli   NATURE

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

ChemicalToolBoX and its application on the study of the drug like and purchasable space

(2014) Xavier Lucas et al.   Journal of Cheminformatics

QSAR DataBank - an approach for the digital organization and archiving of QSAR model information

(2014) Villu Ruusmann et al.   Journal of Cheminformatics

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

(2013) R. Ochoa et al.   BIOINFORMATICS

Drug Discovery Applications for KNIME: An Open Source Data Mining Platform

(2013) Michael P. Mazanetz et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

QSAR workbench: automating QSAR modeling to drive compound design

(2013) Richard Cox et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

If We Share Data, Will Anyone Use Them? Data Sharing and Reuse in the Long Tail of Science and Technology

(2013) Jillian C. Wallis et al.   PLoS One

The CARLSBAD Database: A Confederated Database of Chemical Bioactivities

(2013) Stephen L. Mathias et al.   Database-The Journal of Biological Databases and Curation

Ten Simple Rules for Reproducible Computational Research

(2013) Geir Kjetil Sandve et al.   PLoS Computational Biology

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

(2012) Adam Hospital et al.   BIOINFORMATICS

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

The Challenges Involved in Modeling Toxicity Data In Silico: A Review

(2012) M. Paul Gleeson et al.   CURRENT PHARMACEUTICAL DESIGN

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

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

(2012) Lars Ruddigkeit et al.   Journal of Chemical Information and Modeling

Scientific workflow systems: Pipeline Pilot and KNIME

(2012) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predicting New Indications for Approved Drugs Using a Proteochemometric Method

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

Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases

(2012) Johanna M. Jansen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

The data paper: a mechanism to incentivize data publishing in biodiversity science

(2011) Vishwas Chavan et al.   BMC BIOINFORMATICS

Cloud Computing Approaches to Accelerate Drug Discovery Value Chain

(2011) Vibhav Garg et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

(2011) Iurii Sushko et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Automated QSAR with a Hierarchy of Global and Local Models

(2011) David J. Wood et al.   Molecular Informatics

Structural alerts for estimating the carcinogenicity of pesticides and biocides

(2011) J. Devillers et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

AZOrange - High performance open source machine learning for QSAR modeling in a graphical programming environment

(2011) Jonna C Stålring et al.   Journal of Cheminformatics

Profiling the NIH Small Molecule Repository for Compounds That Generate H2O2 by Redox Cycling in Reducing Environments

(2010) Karina M. Soares et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

Chembench: a cheminformatics workbench

(2010) Theo Walker et al.   BIOINFORMATICS

CDK-Taverna: an open workflow environment for cheminformatics

(2010) Thomas Kuhn et al.   BMC BIOINFORMATICS

Principles of early drug discovery

(2010) JP Hughes et al.   BRITISH JOURNAL OF PHARMACOLOGY

Nelfinavir: A magic bullet to annihilate cancer cells

(2010) Wei Wu et al.   CANCER BIOLOGY & THERAPY

QM/MM Approaches in Medicinal Chemistry Research

(2010) Lochana Menikarachchi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Advances in computational methods to predict the biological activity of compounds

(2010) Chanin Nantasenamat et al.   Expert Opinion on Drug Discovery

Reproducible Science

(2010) A. Casadevall et al.   INFECTION AND IMMUNITY

Best Practices for QSAR Model Development, Validation, and Exploitation

(2010) Alexander Tropsha   Molecular Informatics

In silico research in the era of cloud computing

(2010) Joel T Dudley et al.   NATURE BIOTECHNOLOGY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Computational solutions to large-scale data management and analysis

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

Unveiling the role of network and systems biology in drug discovery

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

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

(2010) Ola Spjuth et al.   Journal of Cheminformatics

The Roots of Bioinformatics

(2010) David B. Searls   PLoS Computational Biology

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

FlexServ: an integrated tool for the analysis of protein flexibility

(2009) J. Camps et al.   BIOINFORMATICS

Prepublication data sharing

(2009)   NATURE

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

A Quick Guide to Organizing Computational Biology Projects

(2009) William Stafford Noble   PLoS Computational Biology

Effect of Formal Statistical Significance on the Credibility of Observational Associations

(2008) J. P. A. Ioannidis   AMERICAN JOURNAL OF EPIDEMIOLOGY

Robust Cross-Validation of Linear Regression QSAR Models

(2008) Dmitry A. Konovalov et al.   Journal of Chemical Information and Modeling

The importance of the domain of applicability in QSAR modeling

(2008) Shane Weaver et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

ALREADY LIVE DO NOT PUBLISH Data on display

(2008) Jean-Claude Bradley et al.   NATURE

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

(2008) Chris F Taylor et al.   NATURE BIOTECHNOLOGY

Are the Chemical Structures in Your QSAR Correct?

(2008) Douglas Young et al.   Quantitative structure-activity relationships & combinatorial science

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY