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KNIME molecule viewer nodes
A 3D viewer for large molecules for the KNIME workflow system.
33
mentions
2
contributors
Cite this software
Description
- Provides cheminformatics trying to model proteins within KNIME a way to view them
- Adds nodes to KNIME to visualize proteins, small molecules and pharmacophores
- Adds support to KNIME to handle viewing big molecules
- Used to compare pharmacophore generation tools
- Used to check ligand repurposing
License
Participating organisations
Reference papers
Journal articles
2- 1.Author(s): Albert J. Kooistra, Márton Vass, Ross McGuire, Rob Leurs, Iwan J. P. de Esch, Gert Vriend, Stefan Verhoeven, Chris de GraafPublished in ChemMedChem by Wiley in 2018, page: 614-62610.1002/cmdc.201700754
- 2.Author(s): Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J. P. de Esch, Scott J. Lusher, Rob Leurs, Lars Ridder, Albert J. Kooistra, Tina Ritschel, Chris de GraafPublished in Journal of Chemical Information and Modeling by American Chemical Society (ACS) in 2017, page: 115-12110.1021/acs.jcim.6b00686
Mentions
Book section
4- 1.Author(s): Jonathan D TyzackPublished in Comprehensive Pharmacology by Elsevier in 2022, page: 769-79110.1016/b978-0-12-820472-6.00067-0
- 2.Author(s): Dominique Sydow, Jaime Rodríguez-Guerra, Andrea VolkamerPublished in ACS Symposium Series, Teaching Programming across the Chemistry Curriculum by American Chemical Society in 2021, page: 135-15810.1021/bk-2021-1387.ch010
- 3.Author(s): Albert J. Kooistra, Andrea VolkamerPublished in Annual Reports in Medicinal Chemistry, Platform Technologies in Drug Discovery and Validation by Elsevier in 2017, page: 197-23610.1016/bs.armc.2017.08.001
- 4.Author(s): Márton Vass, Albert J. Kooistra, Stefan Verhoeven, David Gloriam, Iwan J. P. de Esch, Chris de GraafPublished in Methods in Molecular Biology, Computational Methods for GPCR Drug Discovery by Springer New York in 2017, page: 73-11310.1007/978-1-4939-7465-8_4
Journal articles
26- 1.Author(s): Powsali Ghosh, Ashok Kumar, Sushil Kumar SinghPublished in Journal of Computational Chemistry by Wiley in 202510.1002/jcc.70030
- 2.Author(s): Carlos D. Ramírez‐Márquez, José L. Medina‐FrancoPublished in Molecular Informatics by Wiley in 202510.1002/minf.202400337
- 3.Author(s): Ruchira Joshi, Zipeng Zheng, Palak Agarwal, Ma’mon M. Hatmal, Xinmin Chang, Paul Seidler, Ian S. HaworthPublished in Artificial Intelligence Chemistry by Elsevier BV in 2024, page: 10006310.1016/j.aichem.2024.100063
- 4.Author(s): Charlotte A. Hoogstraten, Jan B. Koenderink, Carolijn E. van Straaten, Tom Scheer-Weijers, Jan A.M. Smeitink, Tom J.J. Schirris, Frans G.M. RusselPublished in Toxicology in Vitro by Elsevier BV in 2024, page: 10574010.1016/j.tiv.2023.105740
- 5.Author(s): Tom Dekker, Mathilde A. C. H. Janssen, Christina Sutherland, Rene W. M. Aben, Hans W. Scheeren, Daniel Blanco-Ania, Floris P. J. T. Rutjes, Maikel Wijtmans, Iwan J. P. de EschPublished in ACS Medicinal Chemistry Letters by American Chemical Society (ACS) in 2023, page: 583-59010.1021/acsmedchemlett.2c00503
- 6.Author(s): Dominique Sydow, Jaime Rodríguez-Guerra, Andrea VolkamerPublished in Journal of Open Source Software by The Open Journal in 2022, page: 395110.21105/joss.03951
- 7.Author(s): Tomoki Yonezawa, Tsuyoshi Esaki, Kazuyoshi IkedaPublished in Chem-Bio Informatics Journal by Chem-Bio Informatics Society in 2022, page: 38-4510.1273/cbij.22.38
- 8.Author(s): Alan E. Bilsland, Angelo Pugliese, Justin BowerPublished in RSC Medicinal Chemistry by Royal Society of Chemistry (RSC) in 2022, page: 1205-121110.1039/d2md00152g
- 9.Author(s): Silvia Chines, Christiane Ehrt, Marco Potowski, Felix Biesenkamp, Lars Grützbach, Susanne Brunner, Frederik van den Broek, Shilpa Bali, Katja Ickstadt, Andreas BrunschweigerPublished in Chemical Science by Royal Society of Chemistry (RSC) in 2022, page: 11221-1123110.1039/d2sc02474h
- 10.Author(s): Anuraj NayarisseriPublished in Current Topics in Medicinal Chemistry by Bentham Science Publishers Ltd. in 2020, page: 1651-166010.2174/156802662019200701164759
- 11.Author(s): Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin NantasenamatPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 202010.1186/s13321-020-0408-x
- 12.Author(s): Michael P. Mazanetz, Charlotte H.F. Goode, Ewa I. ChudykPublished in Current Medicinal Chemistry by Bentham Science Publishers Ltd. in 2020, page: 6458-647910.2174/0929867326666190409141016
- 13.Author(s): Georgi K Kanev, Chris de Graaf, Bart A Westerman, Iwan J P de Esch, Albert J KooistraPublished in Nucleic Acids Research by Oxford University Press (OUP) in 2020, page: D562-D56910.1093/nar/gkaa895
- 14.Author(s): Adnane Aouidate, Adib Ghaleb, Samir Chtita, Mohammed Aarjane, Abdellah Ousaa, Hamid Maghat, Abdelouahid Sbai, M’barek Choukrad, Mohammed Bouachrine, Tahar LakhlifiPublished in Journal of Biomolecular Structure and Dynamics by Informa UK Limited in 2020, page: 4522-453510.1080/07391102.2020.1779130
- 15.Author(s): Sankalp Jain, Ulf Norinder, Sylvia E. Escher, Barbara ZdrazilPublished in Chemical Research in Toxicology by American Chemical Society (ACS) in 2020, page: 656-66810.1021/acs.chemrestox.0c00511
- 16.Author(s): Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory Landrum, Andrea VolkamerPublished in Journal of Chemical Information and Modeling by American Chemical Society (ACS) in 2019, page: 4083-408610.1021/acs.jcim.9b00662
- 17.Author(s): Magdalena Galster, Marius Löppenberg, Fabian Galla, Frederik Börgel, Oriana Agoglitta, Johannes Kirchmair, Ralph HollPublished in Tetrahedron by Elsevier BV in 2019, page: 486-50910.1016/j.tet.2018.12.011
- 18.Author(s): Han‐Wen Pei, Aatto LaaksonenPublished in Journal of Computational Chemistry by Wiley in 2019, page: 2539-254910.1002/jcc.26028
- 19.Author(s): Jonathan D. Tyzack, Johannes KirchmairPublished in Chemical Biology & Drug Design by Wiley in 2019, page: 377-38610.1111/cbdd.13445
- 20.Author(s): Filip Miljković, Raquel Rodríguez-Pérez, Jürgen BajorathPublished in Journal of Medicinal Chemistry by American Chemical Society (ACS) in 2019, page: 8738-874810.1021/acs.jmedchem.9b00867
- 21.Author(s): Márton Vass, Albert J. Kooistra, Dehua Yang, Raymond C. Stevens, Ming-Wei Wang, Chris de GraafPublished in Trends in Pharmacological Sciences by Elsevier BV in 2018, page: 494-51210.1016/j.tips.2018.02.004
- 22.Author(s): Christiane Ehrt, Tobias Brinkjost, Oliver KochPublished in PLOS Computational Biology by Public Library of Science (PLoS) in 2018, page: e100648310.1371/journal.pcbi.1006483
- 23.Author(s): Márton Vass, Sabina Podlewska, Iwan J. P. de Esch, Andrzej J. Bojarski, Rob Leurs, Albert J. Kooistra, Chris de GraafPublished in Journal of Medicinal Chemistry by American Chemical Society (ACS) in 2018, page: 3784-383910.1021/acs.jmedchem.8b00836
- 24.Author(s): Filip Miljković, Jürgen BajorathPublished in ACS Omega by American Chemical Society (ACS) in 2018, page: 1147-115310.1021/acsomega.7b01960
- 25.Author(s): Fleur M. Ferguson, Nathanael S. GrayPublished in Nature Reviews Drug Discovery by Springer Science and Business Media LLC in 2018, page: 353-37710.1038/nrd.2018.21
- 26.Author(s): Mariana González-Medina, J. Jesús Naveja, Norberto Sánchez-Cruz, José L. Medina-FrancoPublished in RSC Advances by Royal Society of Chemistry (RSC) in 2017, page: 54153-5416310.1039/c7ra11831g
Other
3- 1.Author(s): Liting Ren, Yitian Bai, Chenyu Shi, Ying Tan, Shuyan Zhao, Qi Li, Daniel J Macqueen, Shikai LiuPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.11.07.622431
- 2.Author(s): Babs Briels, Chris de Graaf, Andreas BenderPublished in Structural Biology in Drug Discovery by Wiley in 2020, page: 53-7710.1002/9781118681121.ch3
- 3.Author(s): Valerie J. GilletPublished in Biomolecular and Bioanalytical Techniques by Wiley in 2019, page: 17-3610.1002/9781119483977.ch2
Testimonials
For such a purposes I used to use 2 very useful nodes (namely Ligands Viewer and Ligands and Proteins Viewer) that were part of the great 3D-e-Chem 3 extension and that could even be integrated into KNIME components.
– https://forum.knime.com/t/3d-ligand-and-protein-visualization-from-knime-5-x/75016
Contributors
Contact person
AK
Albert J. Kooistra
VU University Amsterdam
Netherlands eScience Center
Related projects
3D-e-Chem
Efficient exploitation of the massive amount of modern-day life science data
Updated 26 months ago
Finished