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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

[…] 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. […]


Large scale ligand based predictive modelling using support vector machines

PMCID: 4980776
PMID: 27516811
DOI: 10.1186/s13321-016-0151-5

[…] using a non-linear kernel proved to be infeasible for large data sizes, even with substantial computational resources on a computer cluster. to deploy the resulting models, we extended the bioclipse decision support framework to support models from liblinear and made our models of logd and solubility available from within bioclipse., the online version of this article […]


Collaborative decision support and documentation in chemical safety with KnowSEC

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

[…] 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 […]


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

[…] posed results for each chemical structure, best pose was retained. the resultant best pose score values in the series were used for analysis of docking and interaction (garofalo et al., 2011[]). , 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 […]


Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

PMCID: 4589695
PMID: 26424081
DOI: 10.1093/database/bav094

[…] its components have been designed to be of general use for other developers in the scientific community and it may be integrated into any java gui application, based on swing, swt, eclipse rcp and bioclipse (), and it is interoperable with the cdm library () and biojava api (application programming interface) (). furthermore, support for importing and exporting whole contig alignments […]


Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets

PMCID: 4478615
PMID: 25994950
DOI: 10.1021/acs.jcim.5b00143

[…] datasets for quantitative structure–activity relationships (qsar) have previously been represented in a reproducible way via qsar-ml. these methods also come with a reference implementation for the bioclipse workbench,, which provides a graphical interface. there have been several early efforts at cheminformatics web services; e.g., indiana university provides access to cheminformatics methods […]

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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.