Bioclipse statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Bioclipse

Tool usage distribution map

This map represents all the scientific publications referring to Bioclipse per scientific context
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Associated diseases

This word cloud represents Bioclipse usage per disease context

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Bioclipse specifications


Unique identifier OMICS_04969
Name Bioclipse
Alternative name Bioclipse-R
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Eclipse Public License version 1.0
Computer skills Medium
Version 2.6.2
Stability No
Maintained No


No version available



This tool is not available anymore.

Publications for Bioclipse

Bioclipse citations


Synthesis, characterization, computational studies and biological activity evaluation of Cu, Fe, Co and Zn complexes with 2 butanone thiosemicarbazone and 1,10 phenanthroline ligands as anticancer and antibacterial agents

PMCID: 5938540
PMID: 29743867
DOI: 10.17179/excli2017-984
call_split See protocol

[…] ion 1.4.5 were used to visualize docking poses. All the chemical structures were drawn in Chem Draw Professionals version 15.1. The metabolic sites in the ligands were predicted using Metaprint 2D in Bioclipse version 2.6.2. All the chemicals used in the study were of A.R. grade and purchased from commercial suppliers and used without any further purification. Hydrated salts of metals viz. Cu(CH3C […]


PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

J Cheminform
PMCID: 5861255
PMID: 29556758
DOI: 10.1186/s13321-018-0270-2

[…] . In terms of molecular representation importance, some web servers and stand-alone programs, such as RDKit [], CDK [], rcdk, PaDEL [], Cinfony [], Chemopy [], ChemDes [], BioJava [], BioTriangle [], bioclipse [], propy [], PyDPI [], Biopython, repDNA [], CDK-Taverna [], protr/protrWeb [], ChemmineR [], and Rcpi [] have been established to calculate such descriptors. However, currently available s […]


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

J Cheminform
PMCID: 5461230
DOI: 10.1186/s13321-017-0220-4
call_split See protocol

[…] OSGi bundles are available for the CDK too, which are used by e.g. Bioclipse [, ] and KNIME []. However, because CDK Java packages are occasionally split between CDK modules, the CDK currently needs to be bundled as a single OSGi jar. The bundle is available from htt […]


Large scale ligand based predictive modelling using support vector machines

J Cheminform
PMCID: 4980776
PMID: 27516811
DOI: 10.1186/s13321-016-0151-5
call_split See protocol

[…] Bioclipse is a workbench for the life sciences that provides open source drug discovery functionality []. Bioclipse decision support (DS) [] provides a framework for making predictive models available […]


Collaborative decision support and documentation in chemical safety with KnowSEC

J Cheminform
PMCID: 4842272
PMID: 27110289
DOI: 10.1186/s13321-016-0132-8

[…] Also active users cannot add new decision knowledge to the running system; this holds for tacit decisions added by decision memos but also structured substance data. In [] the decision support system Bioclipse-DS is introduced for supporting the primarily chemical liability assessment. In the shape of an expert system it is focused on the special task of liability assessment. It combines similarit […]


Design, synthesis, in silico toxicity prediction, molecular docking, and evaluation of novel pyrazole derivatives as potential antiproliferative agents

PMCID: 4834670
PMID: 27103897
DOI: 10.17179/excli2016-103

[…] Bioclipse open tox software was run on windows 7 platform, which process the chemical structure by interacting with known toxic compounds for predictive toxicology. Chemical structures were imported i […]

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Bioclipse institution(s)
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden; AstraZeneca Research and Development, Molndal, Sweden; Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
Bioclipse funding source(s)
Supported by the Uppsala University (KoF 07), Swedish VR-2011-6129, and the Swedish strategic research program eSSENCE.

Bioclipse review

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Samuel Lampa

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A very helpful graphical platform for working with primarily Cheminformatics data and tasks. It is an impressive piece of software, that brings together disparate open source software in cheminformatics, into an easy to use graphical client.

A lot of mundane tasks like converting between varous chemical formats, generating 3D models from 2D ones etc, can be done by just right-clicking and selecting operations in menus.

There are some minor quirks, such as that the molecular drawing editor takes a little practice to get used to (after that it works fine though), and occasional very long waiting times when accessing update times etc, that draws away the last star. Otherwise, it is definitely a software worth checking out for the working cheminformatician.