The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (Q30149558)

2

0 references

Christoph Steinbeck

14

0 references

Chris T. Evelo

12

0 references

Rajarshi Guha

13

0 references

Nina Jeliazkova

6

0 references

Ola Spjuth

10

0 references

Stefan Kuhn

7

0 references

Lars Carlsson

5

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Gilleain Torrance

11

0 references

Jonathan Alvarsson

3

0 references

Tomáš Pluskal

Tomáš Pluskal

8

0 references

Arvid Berg

4

Arvid Berg

0 references

Miquel Rojas-Chertó

9

Journal of Cheminformatics

Miquel Rojas-Chertó

0 references

language of work or name

1 reference

6 June 2017

0 references

number of pages

19

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published in

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volume

9

0 references

issue

1

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copyright license

Creative Commons Attribution 4.0 International

start time

6 June 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

on focus list of Wikimedia project

ScienceSource

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/s13321-017-0220-4

0 references

cites work

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

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The Blue Obelisk-interoperability in chemical informatics

3 June 2018

1 reference

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The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics

3 June 2018

has goal

extends the cited work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

3 June 2018

has goal

extends the cited work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Cinfony – combining Open Source cheminformatics toolkits behind a common interface

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Chemical Informatics Functionality in R

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

New developments on the cheminformatics open workflow environment CDK-Taverna

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

KNIME-CDK: Workflow-driven cheminformatics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

LICSS - a chemical spreadsheet in microsoft excel

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

OMG: Open Molecule Generator

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Small Molecule Subgraph Detector (SMSD) toolkit

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

In silico fragmentation for computer assisted identification of metabolite mass spectra

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Bioclipse: an open source workbench for chemo- and bioinformatics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Bioclipse 2: a scriptable integration platform for the life sciences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Applications of the InChI in cheminformatics with the CDK and Bioclipse

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Efficient ring perception for the Chemistry Development Kit

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Open source drug discovery with Bioclipse

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Basic primitives for molecular diagram sketching

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Elemental composition determination based on MSn

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Ring Perception Using Breadth-First Search

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Fast and Scriptable Molecular Graphics in Web Browsers without Java3D

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

The ChEMBL bioactivity database: an update

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Comparing structural fingerprints using a literature-based similarity benchmark

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Extended-connectivity fingerprints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

CML: Evolution and design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

BRENDA in 2017: new perspectives and new tools in BRENDA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Modelling Chemical Reasoning to Predict and Invent Reactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

ReactPRED: a tool to predict and analyze biochemical reactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Ambit-Tautomer: An Open Source Tool for Tautomer Generation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Rendering Molecular Sketches for Publication Quality Output

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Visual Analysis of Biological Activity Data with Scaffold Hunter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Network-analysis-guided synthesis of weisaconitine D and liljestrandinine.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Scaling predictive modeling in drug development with cloud computing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Ligand-based target prediction with signature fingerprints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

WhichCyp: prediction of cytochromes P450 inhibition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Integrated decision support for assessing chemical liabilities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Interactive exploration of chemical space with Scaffold Hunter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Chemical substructures that enrich for biological activity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

Counterexamples in chemical ring perception.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5461230

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Benchmarking study of parameter variation when using signature fingerprints together with support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Highly accurate chemical formula prediction tool utilizing high-resolution mass spectra, MS/MS fragmentation, heuristic rules, and isotope pattern matching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

SIRIUS: decomposing isotope patterns for metabolite identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Jmol– a paradigm shift in crystallographic visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

The FPS fingerprint format and chemfp toolkit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13321-017-0220-4

Faster Mass Decomposition

21 January 2018

1 reference

https://opencitations.net/index/coci/api/v1/references/10.1186/S13321-017-0220-4

Edition 1.4.1-0 of Groovy Cheminformatics with the Chemistry Development Kit

3 September 2022

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics

80

0 references

1 reference

https://opencitations.net/index/api/v1/references/10.1186/S13321-017-0220-4

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

18 January 2024

1 reference

https://opencitations.net/index/api/v1/references/10.1186/S13321-017-0220-4

Making SharePoint® Chemically Aware™.

18 January 2024

1 reference

https://opencitations.net/index/api/v1/references/10.1186/S13321-017-0220-4

10.1186/S13321-017-0220-4

18 January 2024

Identifiers

DOI

0 references

DBLP publication ID

journals/jcheminf/WillighagenMABC17

1 reference

DBLP Dataset 2021-01-02