Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: rdkit
https://packages.ecosyste.ms/registries/pypi.org/packages/rdkit
A collection of chemoinformatics and machine-learning software written in C++ and Python
15 versions
Latest release: about 1 year ago
190 dependent packages
208,051 downloads last month
Papers Mentioning rdkit 27
10.1039/d0sc05337f
A data-driven perspective on the colours of metal–organic frameworksCited by: 14
Author(s): Kevin Maik Jablonka, Seyed Mohamad Moosavi, Mehrdad Asgari, Christopher P. Ireland, Luc Patiny, Berend Smit
Software Mentions: 14
Published: almost 4 years ago
10.1371/journal.pcbi.1008724
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationshipsCited by: 81
Author(s): Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, F. Diblen, Simon Rogers, Justin J. J. van der Hooft
Software Mentions: 9
Published: over 3 years ago
10.3390/ijms22062846
Predicting Potential Endocrine Disrupting Chemicals Binding to Estrogen Receptor α (ERα) Using a Pipeline Combining Structure-Based and Ligand-Based in Silico MethodsCited by: 5
Author(s): Asma Sellami, Matthieu Montès, Nathalie Lagarde
Software Mentions: 5
Published: over 3 years ago
10.3390/ijms20205062
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction DataCited by: 6
Author(s): Ennys Gheyouche, Romain Launay, Jean Lethiec, Antoine Labeeuw, Caroline Roze, Alan Amossé, Stéphane Teletchea
Software Mentions: 4
Published: about 5 years ago
10.3390/ijms21207648
Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein–Inhibitor Complexes in Relevance to Developing Parkinson’s TherapeuticsCited by: 8
Author(s): Natarajan Arul Murugan, Charuvaka Muvva, Chitra Jeyarajpandian, Jeyaraman Jeyakanthan, V. Subramanian
Software Mentions: 4
Published: about 4 years ago
10.3390/ijms21165847
Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer TherapiesCited by: 11
Author(s): Oliver Snow, Nada Lallous, Martin Ester, Artem Cherkasov
Software Mentions: 4
Published: about 4 years ago
10.1007/s10822-021-00405-6
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challengeCited by: 9
Author(s): Eelke B. Lenselink, Pieter F. W. Stouten
Software Mentions: 4
Published: over 3 years ago
10.1080/14686996.2017.1401424
ChemTS: an efficient python library for <i>de novo</i> molecular generationCited by: 170
Author(s): Xiufeng Yang, Jinzhe Zhang, Kazuki Yoshizoe, Kei Terayama, Koji Tsuda
Software Mentions: 3
Published: almost 7 years ago
10.1080/14756366.2016.1260565
Exploring the first Rimonabant analog-opioid peptide hybrid compound, as bivalent ligand for CB1 and opioid receptorsCited by: 26
Author(s): Adriano Mollica, Sveva Pelliccia, Valeria Famiglini, Azzurra Stefanucci, Giorgia Macedonio, Annalisa Chiavaroli, Giustino Orlando, Luigi Brunetti, Claudio Ferrante, Stefano Pieretti, Ettore Novellino, Sándor Benyhe, Ferenc Zádor, Anna Erdei, Edina Szűcs, Reza Samavati, Szalbolch Dvrorasko, Csaba Tömböly, Rino Ragno, Alexandros Patsilinakos, Romano Silvestri
Software Mentions: 3
Published: almost 8 years ago
10.1186/s13321-015-0078-2
Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery fieldCited by: 120
Author(s): Maciej Wójcikowski, Piotr Zielenkiewicz, Paweł Siedlecki
Software Mentions: 3
Published: over 9 years ago
10.3390/ijms22157773
BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein SpaceCited by: 1
Author(s): Neann Mathai, Conrad Stork, Johannes Kirchmair
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1008653
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinationsCited by: 66
Author(s): Liu Qiao, Lei Xie
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0250620
A computational method for drug sensitivity prediction of cancer cell lines based on various molecular informationCited by: 8
Author(s): Fatemeh Ahmadi Moughari, Changiz Eslahchi
Software Mentions: 2
Published: over 3 years ago
10.1039/c9sc04606b
DeltaDelta neural networks for lead optimization of small molecule potencyCited by: 44
Author(s): José Jiménez-Luna, Laura Pérez‐Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13321-019-0381-4
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energiesCited by: 16
Author(s): Christoph Bauer, Gisbert Schneider, Andreas H. Göller
Software Mentions: 2
Published: about 5 years ago
10.1186/s13321-021-00487-2
MAIP: a web service for predicting blood‐stage malaria inhibitorsCited by: 14
Author(s): Nicolas Bosc, Eloy Félix, Ricardo Arcila, David Méndez, Martin Saunders, Darren V. S. Green, Jason Ochoada, Anang A. Shelat, Éric Martin, Preeti Iyer, Ola Engkvist, Andreas Verras, James Duffy, Jeremy N. Burrows, Mark Gardner, Andrew R. Leach
Software Mentions: 2
Published: over 3 years ago
10.1186/s13321-021-00494-3
Using GANs with adaptive training data to search for new moleculesCited by: 18
Author(s): Andrew E. Blanchard, Christopher B. Stanley, Debsindhu Bhowmik
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-81486-z
Chemoprotective antimalarials identified through quantitative high-throughput screening of Plasmodium blood and liver stage parasitesCited by: 12
Author(s): Dorjbal Dorjsuren, Richard T. Eastman, Kathryn J. Wicht, Daniel J. Jansen, Daniel C. Talley, Benjamin A Sigmon, Alexey Zakharov, Norma Roncal, Andrew T. Girvin, Yevgeniya Antonova‐Koch, Paul M Will, Pranav Shah, Hongmao Sun, Carleen Klumpp‐Thomas, Sachel Mok, Tomas Yeo, Stephan Meister, Juan Marugán, Leila Ross, Xin Xu, David J. Maloney, Ajit Jadhav, Bryan T. Mott, Richard J Sciotti, Elizabeth A. Winzeler, Norman C. Waters, Robert F. Campbell, Wenwei Huang, Anton Simeonov, David A. Fidock
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms22041573
Predicting Potential SARS-COV-2 Drugs—In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and DockingCited by: 23
Author(s): Nischal Karki, Niraj Verma, Francesco Trozzi, Peng Tao, Elfi Kraka, Brian D. Zoltowski
Software Mentions: 2
Published: almost 4 years ago
10.3390/metabo10060237
QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and MetabolomicsCited by: 27
Author(s): Bradley C. Naylor, J. Leon Catrow, J. Alan Maschek, James E. Cox
Software Mentions: 2
Published: over 4 years ago
10.1039/c9sc03414e
DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representationsCited by: 119
Author(s): Ahmet Süreyya Rifaioglu, Esra Nalbat, Volkan Atalay, Maria Jesus Martin, Rengül Cetin-Atalay, Tunca Doğan
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0254429
Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilumCited by: 3
Author(s): Yuanyue Li, Michael Kuhn, Joanna Zukowska-Kasprzyk, Marco L. Hennrich, Panagiotis L. Kastritis, Francis J. O’Reilly, Prasad Phapale, Martin Beck, Anne‐Claude Gavin, Peer Bork
Software Mentions: 1
Published: over 3 years ago
10.3390/ijms22147714
Support Vector Machine as a Supervised Learning for the Prioritization of Novel Potential SARS-CoV-2 Main Protease InhibitorsCited by: 8
Author(s): Nedra Mekni, Claudia Coronnello, Thomas Langer, Maria de Lurdes Pereira Rosa, Ugo Perricone
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules26185451
Azocalix[4]arene-Rhodamine Supramolecular Hypoxia-Sensitive Systems: A Search for the Best Calixarene Hosts and Rhodamine GuestsCited by: 9
Author(s): Diana A. Mironova, Vladimir Burilov, Farida Galieva, Mohamed Khalifa, Sofia Kleshnina, Alsu Gazalieva, Ramil Nugmanov, S. E. Solovieva, И. С. Антипин
Software Mentions: 1
Published: about 3 years ago
10.3390/ijms22084023
A Cascade Graph Convolutional Network for Predicting Protein–Ligand Binding AffinityCited by: 11
Author(s): Hui-Min Shen, Zhang You-zhi, Chun-Hou Zheng, Bing Wang, Youzhi Zhang
Software Mentions: 1
Published: over 3 years ago
10.1038/s41392-021-00568-6
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19Cited by: 77
Author(s): Yiyue Ge, Tingzhong Tian, Suling Huang, Fangping Wan, Jingxin Li, Shuya Li, Xiaoting Wang, Hui Yang, Lixiang Hong, Nian Wu, Enming Yuan, Ying Luo, Lili Cheng, Chengliang Hu, Yipin Lei, Hantao Shu, Xiaolong Feng, Ziyuan Jiang, Yunfu Wu, Ying Cheng, Xiling Guo, Lunbiao Cui, Xiao Liang, Li Zeng, Chunhao Yang, Ze‐Hong Miao, Ligong Chen, Haitao Li, Hainian Zeng, Dan Zhao, Fengcai Zhu, Xiaoxia Shen, Jianyang Zeng
Software Mentions: 1
Published: over 3 years ago
10.1126/sciadv.aax1950
Molecular docking with Gaussian Boson SamplingCited by: 79
Author(s): Leonardo Banchi, Mark Fingerhuth, Tomáš Babej, Christopher Ing, Juan Miguel Arrazola
Software Mentions: 1
Published: over 4 years ago