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: bioconductor: ChemmineR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/ChemmineR
Cheminformatics Toolkit for R
1 version
Latest release: about 1 year ago
8 dependent packages
465,684 downloads total
Papers Mentioning ChemmineR 39
10.3390/metabo9100200
The metaRbolomics Toolbox in Bioconductor and beyondCited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago
10.1371/journal.pone.0244876
Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomesCited by: 12
Author(s): Moamen M. Elmassry, Sunghwan Kim, Ben Busby
Software Mentions: 16
Published: almost 4 years ago
10.1186/s13321-018-0270-2
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactionsCited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0124600
MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and DevelopmentCited by: 36
Author(s): Selçuk Korkmaz, Gökmen Zararsız, Dinçer Göksülük
Software Mentions: 7
Published: over 9 years ago
10.1186/s13321-020-00447-2
DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniquesCited by: 54
Author(s): Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori, Magbubah Essack
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pone.0171413
Large-scale bioactivity analysis of the small-molecule assayed proteomeCited by: 4
Author(s): Tyler W. H. Backman, Daniel S. Evans, Thomas Girke
Software Mentions: 5
Published: over 7 years ago
10.21203/rs.3.rs-25643/v1
Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCSCited by: 5
Author(s): Sinead M. O’Donovan, Hunter M. Eby, Nicholas Henkel, Justin Creeden, Ali Sajid Imami, Sophie Asah, Xiaolu Zhang, Xiaojun Wu, Rawan Alnafisah, R Travis Taylor, James Reigle, Alexander W. Thorman, Behrouz Shamsaei, Jarek Meller, Robert E. McCullumsmith
Software Mentions: 5
Published: over 4 years ago
10.1038/s41598-019-47094-8
Odors from phylogenetically-distant plants to Brassicaceae repel an herbivorous Brassica specialistCited by: 11
Author(s): Chase A. Stratton, Elisabeth A. Hodgdon, Cesar Rodriguez‐Saona, Anthony M. Shelton, Yolanda H. Chen
Software Mentions: 5
Published: over 5 years ago
10.1007/s10822-017-0049-y
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2Cited by: 94
Author(s): Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikaël Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel‐Touris, Adrien Melquiond, Cunliang Geng, Jörg Schaarschmidt, Xue Li, Anna Vangone, Alexandre M. J. J. Bonvin
Software Mentions: 4
Published: about 7 years ago
10.3390/toxins11110631
Calm Before the Storm: A Glimpse into the Secondary Metabolism of Aspergillus welwitschiae, the Etiologic Agent of the Sisal Bole RotCited by: 6
Author(s): Gabriel Quintanilha-Peixoto, Rosimére Oliveira Torres, Isabella Mary Alves Reis, Thiago Alves Santos de Oliveira, Dener Eduardo Bortolini, Elizabeth Amélia Alves Duarte, Vasco Azevedo, Bertram Brenig, Eric Roberto Guimarães Rocha Aguiar, Ana Cristina Fermino Soares, Aristóteles Goés-Neto, Alexsandro Branco
Software Mentions: 4
Published: about 5 years ago
10.26508/lsa.201800098
An integrative machine learning approach for prediction of toxicity-related drug safetyCited by: 38
Author(s): Artem Lysenko, Alok Sharma, Keith A. Boroevich, Tatsuhiko Tsunoda
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-015-2165-1
An integrative analysis of small molecule transcriptional responses in the human malaria parasite Plasmodium falciparumCited by: 12
Author(s): Geoffrey H. Siwo, Roger S. Smith, Aiping Tan, Katrina A. Button-Simons, Lisa A. Checkley, Michael T. Ferdig
Software Mentions: 4
Published: almost 9 years ago
10.18632/oncotarget.25966
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targetsCited by: 24
Author(s): Nathalie Lagarde, Julien Rey, Aram G. Gyulkhandanyan, Pierre Tufféry, Maria A. Miteva, Bruno O. Villoutreix
Software Mentions: 3
Published: about 6 years ago
10.1016/j.jbc.2021.100956
OdoriFy: A conglomerate of artificial intelligence–driven prediction engines for olfactory decodingCited by: 12
Author(s): Ria Gupta, Aayushi Mittal, V. P. Agrawal, Samarth Gupta, Kavya Gupta, Rishi Raj Jain, Prakriti Garg, Sanjay Kumar Mohanty, Riya Sogani, Harshit Singh Chhabra, Vishakha Gautam, Tripti Mishra, Debarka Sengupta, Gaurav Ahuja
Software Mentions: 3
Published: over 3 years ago
10.1007/s00128-016-1800-0
A Market-Basket Approach to Predict the Acute Aquatic Toxicity of Munitions and Energetic MaterialsCited by: 1
Author(s): Lyle D. Burgoon
Software Mentions: 3
Published: over 8 years ago
10.1002/1878-0261.12564
Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activitiesCited by: 22
Author(s): Jieyi Di, Buhong Zheng, Qingfei Kong, Ying Jiang, Siyao Liu, Yang Yang, Xudong Han, Yuqi Sheng, Yunpeng Zhang, Cheng Liang, Junwei Han
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.pone.0084260
Improved Metabolic Health Alters Host Metabolism in Parallel with Changes in Systemic Xeno-Metabolites of Gut OriginCited by: 39
Author(s): Caitlin Campbell, Dmitry Grapov, Oliver Fiehn, Carol J. Chandler, D. D. Burnett, Elisabete Abib Pedroso de Souza, Gretchen A. Casazza, Mary Gustafson, Nancy L. Keim, John W. Newman, Gary R. Hunter, José R. Fernández, W. Timothy Garvey, Mary‐Ellen Harper, Charles L. Hoppel, John K. Meissen, Kohei Take, Sean H. Adams
Software Mentions: 3
Published: almost 11 years ago
10.1093/database/baab011
Development of a biomarker database toward performing disease classification and finding disease interrelationsCited by: 2
Author(s): Shaikh Farhad Hossain, Ming Huang, Naoaki Ono, Aki Morita, Shigehiko Kanaya, Md. Altaf-Ul-Amin
Software Mentions: 3
Published: almost 4 years ago
10.3389/fgene.2020.581668
Identification of Potential Key Agents for Targeting RNA-Dependent RNA Polymerase of SARS-CoV-2 by Integrated Analysis and Virtual Drug ScreeningCited by: 5
Author(s): Shuang Ao, Dan Han, Lei Sun, Yanhong Wu, Shuang Liu, Yaojiang Huang
Software Mentions: 3
Published: almost 4 years ago
10.3390/biom11030467
Chemoinformatic Screening for the Selection of Potential Senolytic Compounds from Natural ProductsCited by: 13
Author(s): Oscar Salvador Barrera-Vázquez, Juan Carlos Gómez-Verján, Gil Alfonso Magos-Guerrero
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2105-13-332
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thalianaCited by: 4
Author(s): Gaihua Zhang, Yijing Zhang, Zhen Su
Software Mentions: 2
Published: almost 12 years ago
10.3390/metabo6040031
Metabolomics and Cheminformatics Analysis of Antifungal Function of Plant MetabolitesCited by: 18
Author(s): Miroslava Čuperlović-Culf, Nandhakishore Rajagopalan, Dan Tulpan, Michèle C. Loewen
Software Mentions: 2
Published: about 8 years ago
10.3389/fphar.2017.00880
ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics ApproachesCited by: 41
Author(s): Ashok Sharma, Gopal N. Srivastava, Anirban Roy, Vineet K. Sharma
Software Mentions: 2
Published: almost 7 years ago
10.3389/fphys.2018.00151
Exploration of the Anti-Inflammatory Drug Space Through Network Pharmacology: Applications for Drug RepurposingCited by: 12
Author(s): Guillermo de Anda-Jáuregui, Kai Guo, Brett A. McGregor, Junguk Hur
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-019-50720-0
Modeling cancer drug response through drug-specific informative genesCited by: 37
Author(s): Luca Parca, Gerardo Pepe, Marco Pietrosanto, Giulio Galvan, Leonardo Galli, Antonio Palmeri, Marco Sciandrone, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer‐Citterich
Software Mentions: 2
Published: about 5 years ago
10.1038/s41598-020-77524-x
Virtual screening of anti-HIV1 compounds against SARS-CoV-2: machine learning modeling, chemoinformatics and molecular dynamics simulation based analysisCited by: 36
Author(s): Mahesha Nand, Priyanka Maiti, Tushar Joshi, Subhash Chandra, Veena Pande, Jagdish Chandra Kuniyal, Muthannan Andavar Ramakrishnan
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-021-97031-x
Anthraquinolone and quinolizine derivatives as an alley of future treatment for COVID-19: an in silico machine learning hypothesisCited by: 1
Author(s): Nikhil Samarth, Ritika Kabra, Shailza Singh
Software Mentions: 2
Published: about 3 years ago
10.7554/eLife.01120
Expanding the olfactory code by in silico decoding of odor-receptor chemical spaceCited by: 56
Author(s): Sean Michael Boyle, Shane McInally, Anandasankar Ray
Software Mentions: 2
Published: about 11 years ago
10.3390/ijms21041523
Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning ApproachesCited by: 10
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Huang Hu
Software Mentions: 2
Published: over 4 years ago
10.3390/pathogens10010071
An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical DiseaseCited by: 14
Author(s): Rahul Tyagi, Christina Bulman, Fidelis Cho-Ngwa, Chelsea Fischer, Chris Marcellino, Michelle R. Arkin, James H. McKerrow, Case W. McNamara, Matthew W. Mahoney, Nancy Tricoche, Shabnam Jawahar, James W. Janetka, Sara Lustigman, Judy Sakanari, Makedonka Mitreva
Software Mentions: 1
Published: almost 4 years ago
10.15252/msb.20156400
A chemical–genetic interaction map of small molecules using high‐throughput imaging in cancer cellsCited by: 69
Author(s): Marco Breinig, Felix A. Klein, Wolfgang Huber, Michael Boutros
Software Mentions: 1
Published: almost 9 years ago
10.1155/2015/139254
Development and Mining of a Volatile Organic Compound DatabaseCited by: 27
Author(s): Azian Azamimi Abdullah, Md. Altaf-Ul-Amin, Naoaki Ono, Tetsuo Sato, T. Sugiura, Aki Morita, Tetsuo Katsuragi, Ai Muto, Takaaki Nishioka, Shigehiko Kanaya
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12967-019-1918-z
Computational models for the prediction of adverse cardiovascular drug reactionsCited by: 18
Author(s): Salma Jamal, Waseem Ali, Priya Nagpal, Sonam Grover, Abhinav Grover
Software Mentions: 1
Published: over 5 years ago
10.3389/fcimb.2018.00365
Identification of Anti-staphylococcal and Anti-biofilm Compounds by Repurposing the Medicines for Malaria Venture Pathogen BoxCited by: 4
Author(s): Vasundhra Bhandari, Sourav Chakraborty, Umarani Brahma, Paresh Sharma
Software Mentions: 1
Published: about 6 years ago
10.1098/rsos.160501
PPIMpred: a web server for high-throughput screening of small molecules targeting protein–protein interactionCited by: 10
Author(s): Tanmoy Jana, Abhirupa Ghosh, Sukhen Das Mandal, Raja Banerjee, Sudipto Saha
Software Mentions: 1
Published: over 7 years ago
10.1155/2019/2408126
Active Ingredients and Action Mechanisms of Yi Guan Jian Decoction in Chronic Hepatitis B Patients with Liver FibrosisCited by: 6
Author(s): Guangyao Li, Yuan Zhou, Daniel Man-Yuen Sze, Chao Liu, Qianru Zhang, Zihao Wang, Hua Yu, Ging Chan, Zhongdao Wu, Shi‐Bing Su, Hu Y
Software Mentions: 1
Published: about 5 years ago
10.1038/s41598-017-00908-z
Predicting neurological Adverse Drug Reactions based on biological, chemical and phenotypic properties of drugs using machine learning modelsCited by: 51
Author(s): Salma Jamal, Sumit Goyal, Asheesh Shanker, Abhinav Grover
Software Mentions: 1
Published: over 7 years ago
10.1038/s41598-019-45548-7
Identification of small molecule enzyme inhibitors as broad-spectrum anthelminticsCited by: 18
Author(s): Rahul Tyagi, Mostafa A. Elfawal, Scott A. Wildman, Jon Helander, Christina Bulman, Judy Sakanari, Bruce A. Rosa, Paul J. Brindley, James W. Janetka, Raffi V. Aroian, Makedonka Mitreva
Software Mentions: 1
Published: over 5 years ago