cran: rcdk | Projects | Ecosyste.ms: Papers

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

10.1186/s13321-020-00477-w

patRoon: open source software platform for environmental mass spectrometry based non-target screening
Cited by: 76
Author(s): Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, P. de Voogt, Emma L. Schymanski
Software Mentions: 20
Published: almost 4 years ago

10.1186/s13321-015-0094-2

RRegrs: an R package for computer-aided model selection with multiple regression models
Cited by: 40
Author(s): Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernández-Lozano, Haralambos Sarimveis, Egon Willighagen
Software Mentions: 10
Published: over 9 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.0196865

Predicting potential drug-drug interactions on topological and semantic similarity features using statistical learning
Cited by: 89
Author(s): Andrej Kastrin, Polonca Ferk, Brane Leskošek
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pcbi.1009302

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge
Cited by: 5
Author(s): Zhitao Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug Dream Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
Software Mentions: 7
Published: over 3 years ago

10.3390/molecules25246057

QSAR Model for Predicting the Cannabinoid Receptor 1 Binding Affinity and Dependence Potential of Synthetic Cannabinoids
Cited by: 5
Author(s): Won Young Lee, So‐Jung Park, Ji-Young Hwang, Choon‐Gon Jang, Yong Sup Lee, Jongmin Kim, Xiaodi Zhao, Aekyung Park, Kyung Hoon Min, Choon‐Gon Jang, Hyun-Ju Park
Software Mentions: 7
Published: about 4 years ago

10.1186/s13321-015-0086-2

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules
Cited by: 36
Author(s): Daniel S. Murrell, Isidro Cortés-Ciriano, Gerard J. P. van Westen, Ian P. Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen
Software Mentions: 7
Published: over 9 years ago

10.3390/molecules25112615

The Study on the hERG Blocker Prediction Using Chemical Fingerprint Analysis
Cited by: 21
Author(s): Kwang-Eun Choi, Anand Balupuri, Nam Sook Kang
Software Mentions: 6
Published: over 4 years ago

10.1128/mSystems.00187-19

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
Cited by: 10
Author(s): Joseph P. Webb, V S Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony R. Larson, Kathryn S. Lilley, Graham R. Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
Software Mentions: 4
Published: over 5 years ago

10.1186/s13321-019-0405-0

The rcdk and cluster R packages applied to drug candidate selection
Cited by: 24
Author(s): Adrian Voicu, Narcis Duţeanu, Mirela Voicu, Daliborca Vlad, Victor Dumitraşcu
Software Mentions: 4
Published: almost 5 years ago

10.1007/s11306-014-0727-x

Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics
Cited by: 76
Author(s): Mingshu Cao, Karl Fraser, Jan Huege, Tom Featonby, Susanne Rasmussen, Chris S. Jones
Software Mentions: 3
Published: over 10 years ago

10.3389/fnut.2020.602515

Challenges Associated With the Design and Deployment of Food Intake Urine Biomarker Technology for Assessment of Habitual Diet in Free-Living Individuals and Populations—A Perspective
Cited by: 2
Author(s): Manfred Beckmann, Thomas Wilson, Amanda J. Lloyd, Duarte Torres, A. Góios, Naomi D. Willis, Laura Lyons, Helen Phillips, John C. Mathers, John Draper
Software Mentions: 3
Published: about 4 years ago

10.1186/s13321-019-0383-2

SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data
Cited by: 59
Author(s): Domenico Gadaleta, Kristijan Vuković, Cosimo Toma, Giovanna J. Lavado, Agnes L. Karmaus, Nicole Kleinstreuer, Emilio Benfenati, Alessandra Roncaglioni
Software Mentions: 3
Published: over 5 years ago

10.1186/s13321-018-0309-4

chemmodlab: a cheminformatics modeling laboratory R package for fitting and assessing machine learning models
Cited by: 2
Author(s): Jeremy R. Ash, Jacqueline M. Hughes‐Oliver
Software Mentions: 3
Published: about 6 years ago

10.1186/s13321-018-0297-4

Probing the chemical–biological relationship space with the Drug Target Explorer
Cited by: 9
Author(s): Robert J. Allaway, Salvatore La Rosa, Justin Guinney
Software Mentions: 3
Published: over 6 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

10.1371/journal.pone.0226770

MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra
Cited by: 21
Author(s): Youzhong Liu, Aida Mrzic, Pieter Meysman, Thomas De Vijlder, Edwin P. Romijn, Dirk Valkenborg, Wout Bittremieux, Kris Laukens
Software Mentions: 2
Published: almost 5 years ago

10.1186/1758-2946-5-30

Drug repositioning: a machine-learning approach through data integration
Cited by: 255
Author(s): Francesco Napolitano, Yan Zhao, Vânia M. Moreira, Roberto Tagliaferri, Juha Kere, Mauro D’Amato, Dario Greco
Software Mentions: 2
Published: over 11 years ago

10.1186/s13321-017-0220-4

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
Cited by: 254
Author(s): Egon Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kühn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain M. Torrance, Chris T. Evelo, Rajarshi Guha, Christoph Steinbeck
Software Mentions: 2
Published: over 7 years ago

10.1155/2020/4795140

Machine-Learning Prediction of Oral Drug-Induced Liver Injury (DILI) via Multiple Features and Endpoints
Cited by: 9
Author(s): Xiaobin Liu, Danhua Zheng, Yingying Zhong, Zhaofan Xia, Heng Luo, Zuquan Weng
Software Mentions: 2
Published: over 4 years ago

10.3389/fphar.2020.00639

Dual Transcriptomic and Molecular Machine Learning Predicts all Major Clinical Forms of Drug Cardiotoxicity
Cited by: 11
Author(s): Polina Mamoshina, Alfonso Bueno‐Orovio, Blanca Rodriguez
Software Mentions: 1
Published: over 4 years ago

10.1093/bioinformatics/btaa998

Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
Cited by: 7
Author(s): Eric Bach, Simon Rogers, John Williamson, Juho Rousu
Software Mentions: 1
Published: about 4 years ago

10.3390/metabo11050284

Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode
Cited by: 18
Author(s): Liesa Salzer, Michael Witting
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1005678

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
Cited by: 78
Author(s): Anna Cichońska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0005359

Dihydrobenz[e][1,4]oxazepin-2(3H)-ones, a new anthelmintic chemotype immobilising whipworm and reducing infectivity in vivo
Cited by: 35
Author(s): Frederick A. Partridge, Erin A. Murphy, Nicky J. Willis, Carole J. R. Bataille, Ruth Forman, Narinder Heyer-Chauhan, Bruno Marinič, Daniel J. C. Sowood, Graham M. Wynne, Kathryn J. Else, Angela J. Russell, David B. Sattelle
Software Mentions: 1
Published: almost 8 years ago

10.1093/bioinformatics/bts681

Bioclipse-R: integrating management and visualization of life science data with statistical analysis
Cited by: 9
Author(s): Ola Spjuth, Valentin Georgiev, Lars Carlsson, Jonathan Alvarsson, Arvid Berg, Egon Willighagen, Jarl E. S. Wikberg, Martin Eklund
Software Mentions: 1
Published: about 12 years ago

10.1007/s10822-016-0008-z

Bayesian molecular design with a chemical language model
Cited by: 103
Author(s): Hisaki Ikebata, Kenta Hongo, Tetsu Isomura, Ryo Maezono, Ryo Yoshida
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep35996

DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome
Cited by: 24
Author(s): Heng Luo, Ping Zhang, Xi Cao, Dizheng Du, Ya Hao, Hui Huang, Can Li, Shengying Qin, Chunling Wan, Leming Shi, Lin He, Lun Yang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-18025-2

iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting
Cited by: 84
Author(s): Farshid Rayhan, Sajid Ahmed, Swakkhar Shatabda, Dewan Md. Farid, Zaynab Mousavian, Abdollah Dehzangi, M. Sohel Rahman
Software Mentions: 1
Published: about 7 years ago

Ecosyste.ms: Papers

Projects: cran: rcdk

Papers Mentioning rcdk 30