Literature DB >> 33858509

QSAR-Co-X: an open source toolkit for multitarget QSAR modelling.

Amit Kumar Halder1, M Natália Dias Soeiro Cordeiro2.   

Abstract

Quantitative structure activity relationships (QSAR) modelling is a well-known computational tool, often used in a wide variety of applications. Yet one of the major drawbacks of conventional QSAR modelling is that models are set up based on a limited number of experimental and/or theoretical conditions. To overcome this, the so-called multitasking or multitarget QSAR (mt-QSAR) approaches have emerged as new computational tools able to integrate diverse chemical and biological data into a single model equation, thus extending and improving the reliability of this type of modelling. We have developed QSAR-Co-X, an open source python-based toolkit (available to download at https://github.com/ncordeirfcup/QSAR-Co-X ) for supporting mt-QSAR modelling following the Box-Jenkins moving average approach. The new toolkit embodies several functionalities for dataset selection and curation plus computation of descriptors, for setting up linear and non-linear models, as well as for a comprehensive results analysis. The workflow within this toolkit is guided by a cohort of multiple statistical parameters and graphical outputs onwards assessing both the predictivity and the robustness of the derived mt-QSAR models. To monitor and demonstrate the functionalities of the designed toolkit, four case-studies pertaining to previously reported datasets are examined here. We believe that this new toolkit, along with our previously launched QSAR-Co code, will significantly contribute to make mt-QSAR modelling widely and routinely applicable.

Entities:  

Keywords:  Feature selection; Machine learning; Multitarget models; QSAR; Software tools

Year:  2021        PMID: 33858509     DOI: 10.1186/s13321-021-00508-0

Source DB:  PubMed          Journal:  J Cheminform        ISSN: 1758-2946            Impact factor:   5.514


  18 in total

Review 1.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

2.  QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models.

Authors:  Pravin Ambure; Amit Kumar Halder; Humbert González Díaz; M Natália D S Cordeiro
Journal:  J Chem Inf Model       Date:  2019-05-24       Impact factor: 4.956

Review 3.  Advanced In Silico Approaches for Drug Discovery: Mining Information from Multiple Biological and Chemical Data Through mtk- QSBER and pt-QSPR Strategies.

Authors:  Alejandro Speck-Planche; Maria Natália Dias Soeiro Cordeiro
Journal:  Curr Med Chem       Date:  2017       Impact factor: 4.530

4.  BET bromodomain inhibitors: fragment-based in silico design using multi-target QSAR models.

Authors:  Alejandro Speck-Planche; Marcus T Scotti
Journal:  Mol Divers       Date:  2018-11-12       Impact factor: 2.943

5.  Recent advances in fragment-based computational drug design: tackling simultaneous targets/biological effects.

Authors:  Alejandro Speck-Planche
Journal:  Future Med Chem       Date:  2018-07-30       Impact factor: 3.808

6.  Biliary cystadenoma of the liver. (A case report).

Authors:  K C Kokal; P Abraham; B D Pimparkar; A P Desai; R D Bapat
Journal:  J Postgrad Med       Date:  1983-01       Impact factor: 1.476

7.  Enabling the Discovery and Virtual Screening of Potent and Safe Antimicrobial Peptides. Simultaneous Prediction of Antibacterial Activity and Cytotoxicity.

Authors:  Valeria V Kleandrova; Juan M Ruso; Alejandro Speck-Planche; M Natália Dias Soeiro Cordeiro
Journal:  ACS Comb Sci       Date:  2016-07-01       Impact factor: 3.784

8.  QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

Authors:  José R Valdés-Martiní; Yovani Marrero-Ponce; César R García-Jacas; Karina Martinez-Mayorga; Stephen J Barigye; Yasser Silveira Vaz d'Almeida; Hai Pham-The; Facundo Pérez-Giménez; Carlos A Morell
Journal:  J Cheminform       Date:  2017-06-07       Impact factor: 5.514

9.  QSAR-Based Virtual Screening: Advances and Applications in Drug Discovery.

Authors:  Bruno J Neves; Rodolpho C Braga; Cleber C Melo-Filho; José Teófilo Moreira-Filho; Eugene N Muratov; Carolina Horta Andrade
Journal:  Front Pharmacol       Date:  2018-11-13       Impact factor: 5.810

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  3 in total

1.  Multi-Target In Silico Prediction of Inhibitors for Mitogen-Activated Protein Kinase-Interacting Kinases.

Authors:  Amit Kumar Halder; M Natália D S Cordeiro
Journal:  Biomolecules       Date:  2021-11-10

2.  Screening of antibacterial compounds with novel structure from the FDA approved drugs using machine learning methods.

Authors:  Wen-Xing Li; Xin Tong; Peng-Peng Yang; Yang Zheng; Ji-Hao Liang; Gong-Hua Li; Dahai Liu; Dao-Gang Guan; Shao-Xing Dai
Journal:  Aging (Albany NY)       Date:  2022-02-12       Impact factor: 5.682

Review 3.  Moving Average-Based Multitasking In Silico Classification Modeling: Where Do We Stand and What Is Next?

Authors:  Amit Kumar Halder; Ana S Moura; Maria Natália D S Cordeiro
Journal:  Int J Mol Sci       Date:  2022-04-29       Impact factor: 5.923

  3 in total

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