Literature DB >> 32356548

QSAR without borders.

Eugene N Muratov1, 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.   

Abstract

Prediction of chemical bioactivity and physical properties has been one of the most important applications of statistical and more recently, machine learning and artificial intelligence methods in chemical sciences. This field of research, broadly known as quantitative structure-activity relationships (QSAR) modeling, has developed many important algorithms and has found a broad range of applications in physical organic and medicinal chemistry in the past 55+ years. This Perspective summarizes recent technological advances in QSAR modeling but it also highlights the applicability of algorithms, modeling methods, and validation practices developed in QSAR to a wide range of research areas outside of traditional QSAR boundaries including synthesis planning, nanotechnology, materials science, biomaterials, and clinical informatics. As modern research methods generate rapidly increasing amounts of data, the knowledge of robust data-driven modelling methods professed within the QSAR field can become essential for scientists working both within and outside of chemical research. We hope that this contribution highlighting the generalizable components of QSAR modeling will serve to address this challenge.

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Year:  2020        PMID: 32356548      PMCID: PMC8008490          DOI: 10.1039/d0cs00098a

Source DB:  PubMed          Journal:  Chem Soc Rev        ISSN: 0306-0012            Impact factor:   54.564


  217 in total

1.  Relevance Vector Machines: Sparse Classification Methods for QSAR.

Authors:  Frank R Burden; David A Winkler
Journal:  J Chem Inf Model       Date:  2015-07-21       Impact factor: 4.956

2.  Toward structure-based predictive tools for the selection of chiral stationary phases for the chromatographic separation of enantiomers.

Authors:  Robert Sheridan; Wes Schafer; Patrick Piras; Kerstin Zawatzky; Edward C Sherer; Christian Roussel; Christopher J Welch
Journal:  J Chromatogr A       Date:  2016-05-20       Impact factor: 4.759

3.  Intrinsic Bond Energies from a Bonds-in-Molecules Neural Network.

Authors:  Kun Yao; John E Herr; Seth N Brown; John Parkhill
Journal:  J Phys Chem Lett       Date:  2017-06-05       Impact factor: 6.475

Review 4.  Physically interactive robotic technology for neuromotor rehabilitation.

Authors:  Neville Hogan; Hermano I Krebs
Journal:  Prog Brain Res       Date:  2011       Impact factor: 2.453

Review 5.  General theory for multiple input-output perturbations in complex molecular systems. 1. Linear QSPR electronegativity models in physical, organic, and medicinal chemistry.

Authors:  Humberto González-Díaz; Sonia Arrasate; Asier Gómez-SanJuan; Nuria Sotomayor; Esther Lete; Lina Besada-Porto; Juan M Ruso
Journal:  Curr Top Med Chem       Date:  2013       Impact factor: 3.295

6.  Modelling human embryoid body cell adhesion to a combinatorial library of polymer surfaces.

Authors:  V Chandana Epa; Jing Yang; Ying Mei; Andrew L Hook; Robert Langer; Daniel G Anderson; Martyn C Davies; Morgan R Alexander; David A Winkler
Journal:  J Mater Chem       Date:  2012-09-18

7.  Toward interoperable bioscience data.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Eamonn Maguire; Chris Taylor; Oliver Hofmann; Hong Fang; Steffen Neumann; Weida Tong; Linda Amaral-Zettler; Kimberly Begley; Tim Booth; Lydie Bougueleret; Gully Burns; Brad Chapman; Tim Clark; Lee-Ann Coleman; Jay Copeland; Sudeshna Das; Antoine de Daruvar; Paula de Matos; Ian Dix; Scott Edmunds; Chris T Evelo; Mark J Forster; Pascale Gaudet; Jack Gilbert; Carole Goble; Julian L Griffin; Daniel Jacob; Jos Kleinjans; Lee Harland; Kenneth Haug; Henning Hermjakob; Shannan J Ho Sui; Alain Laederach; Shaoguang Liang; Stephen Marshall; Annette McGrath; Emily Merrill; Dorothy Reilly; Magali Roux; Caroline E Shamu; Catherine A Shang; Christoph Steinbeck; Anne Trefethen; Bryn Williams-Jones; Katherine Wolstencroft; Ioannis Xenarios; Winston Hide
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

8.  Use of in vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in vivo toxicity.

Authors:  Alexander Sedykh; Hao Zhu; Hao Tang; Liying Zhang; Ann Richard; Ivan Rusyn; Alexander Tropsha
Journal:  Environ Health Perspect       Date:  2010-10-27       Impact factor: 9.031

9.  Machine learning bandgaps of double perovskites.

Authors:  G Pilania; A Mannodi-Kanakkithodi; B P Uberuaga; R Ramprasad; J E Gubernatis; T Lookman
Journal:  Sci Rep       Date:  2016-01-19       Impact factor: 4.379

10.  PubChem Substance and Compound databases.

Authors:  Sunghwan Kim; Paul A Thiessen; Evan E Bolton; Jie Chen; Gang Fu; Asta Gindulyte; Lianyi Han; Jane He; Siqian He; Benjamin A Shoemaker; Jiyao Wang; Bo Yu; Jian Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971

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  58 in total

1.  Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.

Authors:  E Prabhu Raman; Thomas J Paul; Ryan L Hayes; Charles L Brooks
Journal:  J Chem Theory Comput       Date:  2020-11-17       Impact factor: 6.006

Review 2.  Recent progress on cheminformatics approaches to epigenetic drug discovery.

Authors:  Zoe Sessions; Norberto Sánchez-Cruz; Fernando D Prieto-Martínez; Vinicius M Alves; Hudson P Santos; Eugene Muratov; Alexander Tropsha; José L Medina-Franco
Journal:  Drug Discov Today       Date:  2020-09-30       Impact factor: 7.851

3.  Scientific Opinion of the Scientific Panel on Plant Protection Products and their Residues (PPR Panel) on testing and interpretation of comparative in vitro metabolism studies.

Authors:  Antonio F Hernandez-Jerez; Paulien Adriaanse; Annette Aldrich; Philippe Berny; Tamara Coja; Sabine Duquesne; Andreas Focks; Marina Marinovich; Maurice Millet; Olavi Pelkonen; Silvia Pieper; Aaldrik Tiktak; Christopher J Topping; Anneli Widenfalk; Martin Wilks; Gerrit Wolterink; Ursula Gundert-Remy; Jochem Louisse; Serge Rudaz; Emanuela Testai; Alfonso Lostia; Jean-Lou Dorne; Juan Manuel Parra Morte
Journal:  EFSA J       Date:  2021-12-23

Review 4.  Ab Initio Machine Learning in Chemical Compound Space.

Authors:  Bing Huang; O Anatole von Lilienfeld
Journal:  Chem Rev       Date:  2021-08-13       Impact factor: 60.622

5.  Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies.

Authors:  Ki Hwan Kim
Journal:  J Comput Aided Mol Des       Date:  2021-03-13       Impact factor: 3.686

6.  Ranking-Oriented Quantitative Structure-Activity Relationship Modeling Combined with Assay-Wise Data Integration.

Authors:  Katsuhisa Matsumoto; Tomoyuki Miyao; Kimito Funatsu
Journal:  ACS Omega       Date:  2021-04-28

7.  Exploring the Prominent and Concealed Inhibitory Features for Cytoplasmic Isoforms of Hsp90 Using QSAR Analysis.

Authors:  Magdi E A Zaki; Sami A Al-Hussain; Syed Nasir Abbas Bukhari; Vijay H Masand; Mithilesh M Rathore; Sumer D Thakur; Vaishali M Patil
Journal:  Pharmaceuticals (Basel)       Date:  2022-03-01

8.  ABCpred: a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors.

Authors:  Aijaz Ahmad Malik; Suvash Chandra Ojha; Nalini Schaduangrat; Chanin Nantasenamat
Journal:  Mol Divers       Date:  2021-10-05       Impact factor: 2.943

9.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

10.  Simplifying inverse materials design problems for fixed lattices with alchemical chirality.

Authors:  Guido Falk von Rudorff; O Anatole von Lilienfeld
Journal:  Sci Adv       Date:  2021-05-19       Impact factor: 14.136

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