bioconductor: ChemmineR | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited 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: over 5 years ago

10.1371/journal.pone.0244876

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes
Cited 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 interactions
Cited 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: almost 7 years ago

10.1371/journal.pone.0124600

MLViS: A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development
Cited 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 techniques
Cited 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 proteome
Cited by: 4
Author(s): Tyler W. H. Backman, Daniel S. Evans, Thomas Girke
Software Mentions: 5
Published: almost 8 years ago

10.21203/rs.3.rs-25643/v1

Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCS
Cited 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 specialist
Cited 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 2
Cited 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: over 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 Rot
Cited 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 safety
Cited by: 38
Author(s): Artem Lysenko, Alok Sharma, Keith A. Boroevich, Tatsuhiko Tsunoda
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-015-2165-1

An integrative analysis of small molecule transcriptional responses in the human malaria parasite Plasmodium falciparum
Cited 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: about 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 targets
Cited by: 24
Author(s): Nathalie Lagarde, Julien Rey, Aram G. Gyulkhandanyan, Pierre Tufféry, Maria A. Miteva, Bruno O. Villoutreix
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.100956

OdoriFy: A conglomerate of artificial intelligence–driven prediction engines for olfactory decoding
Cited 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 Materials
Cited 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 activities
Cited 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: over 5 years ago

10.1371/journal.pone.0084260

Improved Metabolic Health Alters Host Metabolism in Parallel with Changes in Systemic Xeno-Metabolites of Gut Origin
Cited 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 interrelations
Cited 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 Screening
Cited by: 5
Author(s): Shuang Ao, Dan Han, Lei Sun, Yanhong Wu, Shuang Liu, Yaojiang Huang
Software Mentions: 3
Published: about 4 years ago

10.3390/biom11030467

Chemoinformatic Screening for the Selection of Potential Senolytic Compounds from Natural Products
Cited by: 13
Author(s): Oscar Salvador Barrera-Vázquez, Juan Carlos Gómez-Verján, Gil Alfonso Magos-Guerrero
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-13-332

CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana
Cited by: 4
Author(s): Gaihua Zhang, Yijing Zhang, Zhen Su
Software Mentions: 2
Published: about 12 years ago

10.3390/metabo6040031

Metabolomics and Cheminformatics Analysis of Antifungal Function of Plant Metabolites
Cited 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 Approaches
Cited by: 41
Author(s): Ashok Sharma, Gopal N. Srivastava, Anirban Roy, Vineet K. Sharma
Software Mentions: 2
Published: about 7 years ago

10.3389/fphys.2018.00151

Exploration of the Anti-Inflammatory Drug Space Through Network Pharmacology: Applications for Drug Repurposing
Cited by: 12
Author(s): Guillermo de Anda-Jáuregui, Kai Guo, Brett A. McGregor, Junguk Hur
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-50720-0

Modeling cancer drug response through drug-specific informative genes
Cited 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 analysis
Cited by: 36
Author(s): Mahesha Nand, Priyanka Maiti, Tushar Joshi, Subhash Chandra, Veena Pande, Jagdish Chandra Kuniyal, Muthannan Andavar Ramakrishnan
Software Mentions: 2
Published: about 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 hypothesis
Cited by: 1
Author(s): Nikhil Samarth, Ritika Kabra, Shailza Singh
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.01120

Expanding the olfactory code by in silico decoding of odor-receptor chemical space
Cited 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 Approaches
Cited by: 10
Author(s): Madhu Sudhana Saddala, Anton Lennikov, Huang Hu
Software Mentions: 2
Published: almost 5 years ago

10.3390/pathogens10010071

An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease
Cited 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 cells
Cited by: 69
Author(s): Marco Breinig, Felix A. Klein, Wolfgang Huber, Michael Boutros
Software Mentions: 1
Published: about 9 years ago

10.1155/2015/139254

Development and Mining of a Volatile Organic Compound Database
Cited 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 reactions
Cited 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 Box
Cited 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 interaction
Cited 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 Fibrosis
Cited 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: over 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 models
Cited 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 anthelmintics
Cited 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

Projects: bioconductor: ChemmineR

Papers Mentioning ChemmineR 39