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Results: 1 to 20 of 97

1.

Open Babel: An open chemical toolbox.

O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR.

J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33.

PMID:
21982300
[PubMed]
Free PMC Article
2.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR.

J Cheminform. 2012 Aug 13;4(1):17. doi: 10.1186/1758-2946-4-17.

PMID:
22889332
[PubMed]
Free PMC Article
3.

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

Hinselmann G, Rosenbaum L, Jahn A, Fechner N, Zell A.

J Cheminform. 2011 Jan 10;3(1):3. doi: 10.1186/1758-2946-3-3.

PMID:
21219648
[PubMed]
Free PMC Article
4.

OrChem - An open source chemistry search engine for Oracle(R).

Rijnbeek M, Steinbeck C.

J Cheminform. 2009 Oct 22;1(1):17. doi: 10.1186/1758-2946-1-17.

PMID:
20298521
[PubMed]
Free PMC Article
5.

Permuting input for more effective sampling of 3D conformer space.

Carta G, Onnis V, Knox AJ, Fayne D, Lloyd DG.

J Comput Aided Mol Des. 2006 Mar;20(3):179-90. Epub 2006 Jul 14.

PMID:
16841235
[PubMed - indexed for MEDLINE]
6.

MyMolDB: a micromolecular database solution with open source and free components.

Xia B, Tai ZF, Gu YC, Li BJ, Ding LS, Zhou Y.

J Comput Chem. 2011 Oct;32(13):2942-8. doi: 10.1002/jcc.21874. Epub 2011 Jul 5.

PMID:
21728180
[PubMed - indexed for MEDLINE]
7.

BALL--biochemical algorithms library 1.3.

Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O.

BMC Bioinformatics. 2010 Oct 25;11:531. doi: 10.1186/1471-2105-11-531.

PMID:
20973958
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Chemical Descriptors Library (CDL): a generic, open source software library for chemical informatics.

Sykora VJ, Leahy DE.

J Chem Inf Model. 2008 Oct;48(10):1931-42. doi: 10.1021/ci800135h. Epub 2008 Sep 20. Review.

PMID:
18803371
[PubMed - indexed for MEDLINE]
9.

MARVIN: a medical research application framework based on open source software.

Rudolph T, Puls M, Anderegg C, Ebert L, Broehan M, Rudin A, Kowal J.

Comput Methods Programs Biomed. 2008 Aug;91(2):165-74. doi: 10.1016/j.cmpb.2008.04.007. Epub 2008 Jun 9.

PMID:
18541330
[PubMed - indexed for MEDLINE]
10.

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

Turewicz M, Deutsch EW.

Methods Mol Biol. 2011;696:179-203. doi: 10.1007/978-1-60761-987-1_11.

PMID:
21063948
[PubMed - indexed for MEDLINE]
11.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091
[PubMed - indexed for MEDLINE]
Free Article
12.

Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.

BMC Bioinformatics. 2007 Feb 22;8:59.

PMID:
17316423
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD.

Bioinformatics. 2006 Apr 1;22(7):874-82. Epub 2006 Jan 12.

PMID:
16410321
[PubMed - indexed for MEDLINE]
Free Article
14.

ChemT, an open-source software for building template-based chemical libraries.

Abreu RM, Froufe HJ, Daniel PO, Queiroz MJ, Ferreira IC.

SAR QSAR Environ Res. 2011 Jul-Sep;22(5-6):603-10. doi: 10.1080/1062936X.2011.604097.

PMID:
21846264
[PubMed - indexed for MEDLINE]
15.

Cinfony--combining Open Source cheminformatics toolkits behind a common interface.

O'Boyle NM, Hutchison GR.

Chem Cent J. 2008 Dec 3;2:24. doi: 10.1186/1752-153X-2-24.

PMID:
19055766
[PubMed]
Free PMC Article
16.

KNIME-CDK: Workflow-driven cheminformatics.

Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C.

BMC Bioinformatics. 2013 Aug 22;14:257. doi: 10.1186/1471-2105-14-257.

PMID:
24103053
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

NAOMI: on the almost trivial task of reading molecules from different file formats.

Urbaczek S, Kolodzik A, Fischer JR, Lippert T, Heuser S, Groth I, Schulz-Gasch T, Rarey M.

J Chem Inf Model. 2011 Dec 27;51(12):3199-207. doi: 10.1021/ci200324e. Epub 2011 Dec 1.

PMID:
22067015
[PubMed - indexed for MEDLINE]
18.

LICSS - a chemical spreadsheet in microsoft excel.

Lawson KR, Lawson J.

J Cheminform. 2012 Feb 2;4(1):3. doi: 10.1186/1758-2946-4-3.

PMID:
22301088
[PubMed]
Free PMC Article
19.

cPath: open source software for collecting, storing, and querying biological pathways.

Cerami EG, Bader GD, Gross BE, Sander C.

BMC Bioinformatics. 2006 Nov 13;7:497.

PMID:
17101041
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

Helmus JJ, Jaroniec CP.

J Biomol NMR. 2013 Apr;55(4):355-67. doi: 10.1007/s10858-013-9718-x. Epub 2013 Mar 2.

PMID:
23456039
[PubMed - indexed for MEDLINE]
Free PMC Article
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