Literature DB >> 22207193

Of possible cheminformatics futures.

Tudor I Oprea1, Olivier Taboureau, Cristian G Bologa.   

Abstract

For over a decade, cheminformatics has contributed to a wide array of scientific tasks from analytical chemistry and biochemistry to pharmacology and drug discovery; and although its contributions to decision making are recognized, the challenge is how it would contribute to faster development of novel, better products. Here we address the future of cheminformatics with primary focus on innovation. Cheminformatics developers often need to choose between "mainstream" (i.e., accepted, expected) and novel, leading-edge tools, with an increasing trend for open science. Possible futures for cheminformatics include the worst case scenario (lack of funding, no creative usage), as well as the best case scenario (complete integration, from systems biology to virtual physiology). As "-omics" technologies advance, and computer hardware improves, compounds will no longer be profiled at the molecular level, but also in terms of genetic and clinical effects. Among potentially novel tools, we anticipate machine learning models based on free text processing, an increased performance in environmental cheminformatics, significant decision-making support, as well as the emergence of robot scientists conducting automated drug discovery research. Furthermore, cheminformatics is anticipated to expand the frontiers of knowledge and evolve in an open-ended, extensible manner, allowing us to explore multiple research scenarios in order to avoid epistemological "local information minimum trap".

Mesh:

Year:  2011        PMID: 22207193     DOI: 10.1007/s10822-011-9535-9

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  21 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Integration of diverse data sources for prediction of adverse drug events.

Authors:  D R Abernethy; J P F Bai; K Burkhart; H-G Xie; P Zhichkin
Journal:  Clin Pharmacol Ther       Date:  2011-11       Impact factor: 6.875

3.  Drug Repurposing from an Academic Perspective.

Authors:  Tudor I Oprea; Julie E Bauman; Cristian G Bologa; Tione Buranda; Alexandre Chigaev; Bruce S Edwards; Jonathan W Jarvik; Hattie D Gresham; Mark K Haynes; Brian Hjelle; Robert Hromas; Laurie Hudson; Debra A Mackenzie; Carolyn Y Muller; John C Reed; Peter C Simons; Yelena Smagley; Juan Strouse; Zurab Surviladze; Todd Thompson; Oleg Ursu; Anna Waller; Angela Wandinger-Ness; Stuart S Winter; Yang Wu; Susan M Young; Richard S Larson; Cheryl Willman; Larry A Sklar
Journal:  Drug Discov Today Ther Strateg       Date:  2011

Review 4.  Computational systems chemical biology.

Authors:  Tudor I Oprea; Elebeoba E May; Andrei Leitão; Alexander Tropsha
Journal:  Methods Mol Biol       Date:  2011

5.  Country-specific chemical signatures of persistent environmental compounds in breast milk.

Authors:  K Krysiak-Baltyn; J Toppari; N E Skakkebaek; T S Jensen; H E Virtanen; K-W Schramm; H Shen; T Vartiainen; H Kiviranta; O Taboureau; S Brunak; K M Main
Journal:  Int J Androl       Date:  2009-09-24

6.  A crowdsourcing evaluation of the NIH chemical probes.

Authors:  Tudor I Oprea; Cristian G Bologa; Scott Boyer; Ramona F Curpan; Robert C Glen; Andrew L Hopkins; Christopher A Lipinski; Garland R Marshall; Yvonne C Martin; Liliana Ostopovici-Halip; Gilbert Rishton; Oleg Ursu; Roy J Vaz; Chris Waller; Herbert Waldmann; Larry A Sklar
Journal:  Nat Chem Biol       Date:  2009-07       Impact factor: 15.040

7.  The automation of science.

Authors:  Ross D King; Jem Rowland; Stephen G Oliver; Michael Young; Wayne Aubrey; Emma Byrne; Maria Liakata; Magdalena Markham; Pinar Pir; Larisa N Soldatova; Andrew Sparkes; Kenneth E Whelan; Amanda Clare
Journal:  Science       Date:  2009-04-03       Impact factor: 47.728

Review 8.  Pulmonary toxicity and environmental contamination: radicals, electron transfer, and protection by antioxidants.

Authors:  Peter Kovacic; Ratnasamy Somanathan
Journal:  Rev Environ Contam Toxicol       Date:  2009       Impact factor: 7.563

9.  The EuroPhysiome, STEP and a roadmap for the virtual physiological human.

Authors:  J W Fenner; B Brook; G Clapworthy; P V Coveney; V Feipel; H Gregersen; D R Hose; P Kohl; P Lawford; K M McCormack; D Pinney; S R Thomas; S Van Sint Jan; S Waters; M Viceconti
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2008-09-13       Impact factor: 4.226

10.  Collaborative development of predictive toxicology applications.

Authors:  Barry Hardy; Nicki Douglas; Christoph Helma; Micha Rautenberg; Nina Jeliazkova; Vedrin Jeliazkov; Ivelina Nikolova; Romualdo Benigni; Olga Tcheremenskaia; Stefan Kramer; Tobias Girschick; Fabian Buchwald; Joerg Wicker; Andreas Karwath; Martin Gütlein; Andreas Maunz; Haralambos Sarimveis; Georgia Melagraki; Antreas Afantitis; Pantelis Sopasakis; David Gallagher; Vladimir Poroikov; Dmitry Filimonov; Alexey Zakharov; Alexey Lagunin; Tatyana Gloriozova; Sergey Novikov; Natalia Skvortsova; Dmitry Druzhilovsky; Sunil Chawla; Indira Ghosh; Surajit Ray; Hitesh Patel; Sylvia Escher
Journal:  J Cheminform       Date:  2010-08-31       Impact factor: 5.514

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  2 in total

1.  Enhancing life cycle chemical exposure assessment through ontology modeling.

Authors:  David E Meyer; Sidney C Bailin; Daniel Vallero; Peter P Egeghy; Shi V Liu; Elaine A Cohen Hubal
Journal:  Sci Total Environ       Date:  2019-12-27       Impact factor: 7.963

2.  ChemProt-2.0: visual navigation in a disease chemical biology database.

Authors:  Sonny Kim Kjærulff; Louis Wich; Jens Kringelum; Ulrik P Jacobsen; Irene Kouskoumvekaki; Karine Audouze; Ole Lund; Søren Brunak; Tudor I Oprea; Olivier Taboureau
Journal:  Nucleic Acids Res       Date:  2012-11-26       Impact factor: 16.971

  2 in total

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