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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
v2.0.3
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- 1.3D‐e‐Chem: Structural Cheminformatics Workflows for Computer‐Aided Drug DiscoveryAuthor(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
- 2.3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual MachineAuthor(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.Prediction of Drug Metabolism: Use of Structural Biology and In Silico ToolsAuthor(s): Jonathan D TyzackPublished in Comprehensive Pharmacology by Elsevier in 2022, page: 769-79110.1016/b978-0-12-820472-6.00067-0
- 2.Teaching Computer-Aided Drug Design Using TeachOpenCADDAuthor(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.Kinase-Centric Computational Drug DevelopmentAuthor(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.A Structural Framework for GPCR Chemogenomics: What’s In a Residue Number?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.COX‐2 Inhibitor Prediction With KNIME: A Codeless Automated Machine Learning‐Based Virtual Screening WorkflowAuthor(s): Powsali Ghosh, Ashok Kumar, Sushil Kumar SinghPublished in Journal of Computational Chemistry by Wiley in 202510.1002/jcc.70030
- 2.KNIME Workflows for Chemoinformatic Characterization of Chemical DatabasesAuthor(s): Carlos D. Ramírez‐Márquez, José L. Medina‐FrancoPublished in Molecular Informatics by Wiley in 202510.1002/minf.202400337
- 3.KNIME workflows for applications in medicinal and computational chemistryAuthor(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.Pyruvate dehydrogenase is a potential mitochondrial off-target for gentamicin based on in silico predictions and in vitro inhibition studiesAuthor(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.An Automated, Open-Source Workflow for the Generation of (3D) Fragment LibrariesAuthor(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.OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS databaseAuthor(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.Benchmark of 3D conformer generation and molecular property calculation for medium-sized moleculesAuthor(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.Implementation of an AI-assisted fragment-generator in an open-source platformAuthor(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.Navigating chemical reaction space – application to DNA-encoded chemistryAuthor(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.Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug DiscoveryAuthor(s): Anuraj NayarisseriPublished in Current Topics in Medicinal Chemistry by Bentham Science Publishers Ltd. in 2020, page: 1651-166010.2174/156802662019200701164759
- 11.Towards reproducible computational drug discoveryAuthor(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.Ligand- and Structure-Based Drug Design and Optimization using KNIMEAuthor(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.KLIFS: an overhaul after the first 5 years of supporting kinase researchAuthor(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.Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluationAuthor(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.Combining In Vivo Data with In Silico Predictions for Modeling Hepatic Steatosis by Using Stratified Bagging and Conformal PredictionAuthor(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.TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME WorkflowsAuthor(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.Phenylethylene glycol-derived LpxC inhibitors with diverse Zn2+-binding groupsAuthor(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.Feature vector clustering molecular pairs in computer simulationsAuthor(s): Han‐Wen Pei, Aatto LaaksonenPublished in Journal of Computational Chemistry by Wiley in 2019, page: 2539-254910.1002/jcc.26028
- 19.Computational methods and tools to predict cytochrome P450 metabolism for drug discoveryAuthor(s): Jonathan D. Tyzack, Johannes KirchmairPublished in Chemical Biology & Drug Design by Wiley in 2019, page: 377-38610.1111/cbdd.13445
- 20.Machine Learning Models for Accurate Prediction of Kinase Inhibitors with Different Binding ModesAuthor(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.Chemical Diversity in the G Protein-Coupled Receptor SuperfamilyAuthor(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.A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)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.Aminergic GPCR–Ligand Interactions: A Chemical and Structural Map of Receptor Mutation DataAuthor(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.Exploring Selectivity of Multikinase Inhibitors across the Human KinomeAuthor(s): Filip Miljković, Jürgen BajorathPublished in ACS Omega by American Chemical Society (ACS) in 2018, page: 1147-115310.1021/acsomega.7b01960
- 25.Kinase inhibitors: the road aheadAuthor(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.Open chemoinformatic resources to explore the structure, properties and chemical space of moleculesAuthor(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.Glycophagy is an ancient bilaterian pathway supporting metabolic adaptation through STBD1 structural evolutionAuthor(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.Structural ChemogenomicsAuthor(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.Applications of Chemoinformatics in Drug DiscoveryAuthor(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
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