4.6 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Multidisciplinary

Modelling Chemical Reasoning to Predict and Invent Reactions

Marwin H. S. Segler et al.

CHEMISTRY-A EUROPEAN JOURNAL (2017)

Article Biochemical Research Methods

Reaction Decoder Tool (RDT): extracting features from chemical reactions

Syed Asad Rahman et al.

BIOINFORMATICS (2016)

Article Automation & Control Systems

Parallel formula generator based on branch-and-bound algorithm for elucidating high resolution mass spectra

Mingjing Zhang et al.

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2016)

Article Biotechnology & Applied Microbiology

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Mingxun Wang et al.

NATURE BIOTECHNOLOGY (2016)

Article Chemistry, Multidisciplinary

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

Jonathan Alvarsson et al.

JOURNAL OF CHEMINFORMATICS (2016)

Article Chemistry, Multidisciplinary

Comparing structural fingerprints using a literature-based similarity benchmark

Noel M. O'Boyle et al.

JOURNAL OF CHEMINFORMATICS (2016)

Article Chemistry, Medicinal

Scaling Predictive Modeling in Drug Development with Cloud Computing

Behrooz Torabi Moghadam et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

Article Multidisciplinary Sciences

Network-analysis-guided synthesis of weisaconitine D and liljestrandinine

C. J. Marth et al.

NATURE (2015)

Article Multidisciplinary Sciences

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

Kai Duehrkop et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Chemistry, Multidisciplinary

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

V. Ruusmann et al.

JOURNAL OF CHEMINFORMATICS (2015)

Article Chemistry, Multidisciplinary

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

Jie Dong et al.

JOURNAL OF CHEMINFORMATICS (2015)

Article Chemistry, Medicinal

Ligand-Based Target Prediction with Signature Fingerprints

Jonathan Alvarsson et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Article Chemistry, Medicinal

Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines

Jonathan Alvarsson et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Article Biochemical Research Methods

EC-BLAST: a tool to automatically search and compare enzyme reactions

Syed Asad Rahman et al.

NATURE METHODS (2014)

Article Biochemistry & Molecular Biology

The ChEMBL bioactivity database: an update

A. Patricia Bento et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Chemistry, Multidisciplinary

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0

Alex M. Clark et al.

JOURNAL OF CHEMINFORMATICS (2014)

Article Chemistry, Multidisciplinary

Efficient ring perception for the Chemistry Development Kit

John W. May et al.

JOURNAL OF CHEMINFORMATICS (2014)

Article Biochemical Research Methods

WhichCyp: prediction of cytochromes P450 inhibition

Michal Rostkowski et al.

BIOINFORMATICS (2013)

Article Chemistry, Medicinal

QSAR investigation of NaV1.7 active compounds using the SVM/Signature approach and the Bioclipse Modeling platform

Ulf Norinder et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2013)

Article Biochemical Research Methods

KNIME-CDK: Workflow-driven cheminformatics

Stephan Beisken et al.

BMC BIOINFORMATICS (2013)

Article Chemistry, Medicinal

Rendering Molecular Sketches for Publication Quality Output

Alex M. Clark

MOLECULAR INFORMATICS (2013)

Article Chemistry, Medicinal

Ambit-Tautomer: An Open Source Tool for Tautomer Generation

Nikolay T. Kochev et al.

MOLECULAR INFORMATICS (2013)

Article Chemistry, Medicinal

Visual Analysis of Biological Activity Data with Scaffold Hunter

Karsten Klein et al.

MOLECULAR INFORMATICS (2013)

Article Biochemistry & Molecular Biology

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Chemistry, Multidisciplinary

Applications of the InChI in cheminformatics with the CDK and Bioclipse

Ola Spjuth et al.

JOURNAL OF CHEMINFORMATICS (2013)

Article Chemistry, Multidisciplinary

The FPS fingerprint format and chemfp toolkit

Andrew Dalke

Journal of Cheminformatics (2013)

Review Chemistry, Medicinal

Open Source Drug Discovery with Bioclipse

Ola Spjuth et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2012)

Article Chemistry, Multidisciplinary

LICSS - a chemical spreadsheet in microsoft excel

Kevin R. Lawson et al.

JOURNAL OF CHEMINFORMATICS (2012)

Article Chemistry, Multidisciplinary

OMG: Open Molecule Generator

Julio E. Peironcely et al.

JOURNAL OF CHEMINFORMATICS (2012)

Article Biochemical Research Methods

Elemental composition determination based on MSn

Miguel Rojas-Cherto et al.

BIOINFORMATICS (2011)

Article Chemistry, Medicinal

Integrated Decision Support for Assessing Chemical Liabilities

Ola Spjuth et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Multidisciplinary

PaDEL-Descriptor: An Open Source Software to Calculate Molecular Descriptors and Fingerprints

Chun Wei Yap

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Chemistry, Multidisciplinary

New developments on the cheminformatics open workflow environment CDK-Taverna

Andreas Truszkowski et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Chemistry, Multidisciplinary

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

Noel M. O'Boyle et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Chemistry, Multidisciplinary

CML: Evolution and design

Peter Murray-Rust et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Chemistry, Multidisciplinary

jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

Georg Hinselmann et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Chemistry, Multidisciplinary

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

Nina Jeliazkova et al.

JOURNAL OF CHEMINFORMATICS (2011)

Article Biochemical Research Methods

In silico fragmentation for computer assisted identification of metabolite mass spectra

Sebastian Wolf et al.

BMC BIOINFORMATICS (2010)

Article Chemistry, Multidisciplinary

Jmol - a paradigm shift in crystallographic visualization

Robert M. Hanson

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2010)

Article Chemistry, Medicinal

Extended-Connectivity Fingerprints

David Rogers et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Chemistry, Multidisciplinary

Basic primitives for molecular diagram sketching

Alex M Clark

Journal of Cheminformatics (2010)

Article Biochemical Research Methods

SIRIUS: decomposing isotope patterns for metabolite identification

Sebastian Boecker et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Bioclipse 2: A scriptable integration platform for the life sciences

Ola Spjuth et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Interactive exploration of chemical space with Scaffold Hunter

Stefan Wetzel et al.

NATURE CHEMICAL BIOLOGY (2009)

Article Chemistry, Multidisciplinary

Small Molecule Subgraph Detector (SMSD) toolkit

Syed Asad Rahman et al.

JOURNAL OF CHEMINFORMATICS (2009)

Article Biochemical Research Methods

DECOMP -: from interpreting mass spectrometry peaks to solving the money changing problem

Sebastian Boecker et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

Chemical substructures that enrich for biological activity

Justin Klekota et al.

BIOINFORMATICS (2008)

Article Chemistry, Multidisciplinary

Cinfony - combining Open Source cheminformatics toolkits behind a common interface

Noel M. O'Boyle et al.

CHEMISTRY CENTRAL JOURNAL (2008)

Article Biochemical Research Methods

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Tobias Kind et al.

BMC BIOINFORMATICS (2007)

Article Biochemical Research Methods

Bioclipse: an open source workbench for chemo- and bioinformatics

Ola Spjuth et al.

BMC BIOINFORMATICS (2007)

Article Chemistry, Medicinal

Blue Obelisk - Interoperability in chemical informatics

Rajarshi Guha et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2006)

Article Chemistry, Medicinal

LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities

D Vidal et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2005)

Article Chemistry, Multidisciplinary

Counterexamples in chemical ring perception

F Berger et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)

Article Chemistry, Multidisciplinary

The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences

JL Faulon et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2004)

Article Chemistry, Multidisciplinary

The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies

JL Faulon et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)

Article Chemistry, Multidisciplinary

The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics

C Steinbeck et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)