Literature DB >> 24943138

Bigger data, collaborative tools and the future of predictive drug discovery.

Sean Ekins1, Alex M Clark, S Joshua Swamidass, Nadia Litterman, Antony J Williams.   

Abstract

Over the past decade we have seen a growth in the provision of chemistry data and cheminformatics tools as either free websites or software as a service commercial offerings. These have transformed how we find molecule-related data and use such tools in our research. There have also been efforts to improve collaboration between researchers either openly or through secure transactions using commercial tools. A major challenge in the future will be how such databases and software approaches handle larger amounts of data as it accumulates from high throughput screening and enables the user to draw insights, enable predictions and move projects forward. We now discuss how information from some drug discovery datasets can be made more accessible and how privacy of data should not overwhelm the desire to share it at an appropriate time with collaborators. We also discuss additional software tools that could be made available and provide our thoughts on the future of predictive drug discovery in this age of big data. We use some examples from our own research on neglected diseases, collaborations, mobile apps and algorithm development to illustrate these ideas.

Entities:  

Mesh:

Year:  2014        PMID: 24943138      PMCID: PMC4198464          DOI: 10.1007/s10822-014-9762-y

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


  104 in total

Review 1.  Informatics resources for tuberculosis--towards drug discovery.

Authors:  Jagadish Chandrabose Sundaramurthi; S Brindha; T B K Reddy; Luke Elizabeth Hanna
Journal:  Tuberculosis (Edinb)       Date:  2011-09-22       Impact factor: 3.131

2.  The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets.

Authors:  Sergey Trepalin; Nikolay Osadchiy
Journal:  J Comput Aided Mol Des       Date:  2005-12-06       Impact factor: 3.686

3.  Sharing chemical information without sharing chemical structure.

Authors:  Brian B Masek; Lingling Shen; Karl M Smith; Robert S Pearlman
Journal:  J Chem Inf Model       Date:  2008-02-07       Impact factor: 4.956

4.  Sharing chemical relationships does not reveal structures.

Authors:  Matthew Matlock; S Joshua Swamidass
Journal:  J Chem Inf Model       Date:  2013-12-16       Impact factor: 4.956

5.  Enhancing the rate of scaffold discovery with diversity-oriented prioritization.

Authors:  S Joshua Swamidass; Bradley T Calhoun; Joshua A Bittker; Nicole E Bodycombe; Paul A Clemons
Journal:  Bioinformatics       Date:  2011-06-17       Impact factor: 6.937

6.  Four disruptive strategies for removing drug discovery bottlenecks.

Authors:  Sean Ekins; Chris L Waller; Mary P Bradley; Alex M Clark; Antony J Williams
Journal:  Drug Discov Today       Date:  2012-10-23       Impact factor: 7.851

7.  A collaborative database and computational models for tuberculosis drug discovery.

Authors:  Sean Ekins; Justin Bradford; Krishna Dole; Anna Spektor; Kellan Gregory; David Blondeau; Moses Hohman; Barry A Bunin
Journal:  Mol Biosyst       Date:  2010-02-09

8.  A practical approach to achieve private medical record linkage in light of public resources.

Authors:  Mehmet Kuzu; Murat Kantarcioglu; Elizabeth Ashley Durham; Csaba Toth; Bradley Malin
Journal:  J Am Med Inform Assoc       Date:  2012-07-30       Impact factor: 4.497

9.  Redefining Cheminformatics with Intuitive Collaborative Mobile Apps.

Authors:  Alex M Clark; Sean Ekins; Antony J Williams
Journal:  Mol Inform       Date:  2012-07-04       Impact factor: 3.353

10.  Open access and open source in chemistry.

Authors:  Matthew H Todd
Journal:  Chem Cent J       Date:  2007-02-19       Impact factor: 4.215

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  12 in total

1.  Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.

Authors:  Stephen J Capuzzi; Ian Sang-June Kim; Wai In Lam; Thomas E Thornton; Eugene N Muratov; Diane Pozefsky; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2017-01-19       Impact factor: 4.956

2.  App-etite for change.

Authors:  Wendy A Warr
Journal:  J Comput Aided Mol Des       Date:  2014-12-17       Impact factor: 3.686

Review 3.  Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB).

Authors:  Sean Ekins; Anna Coulon Spektor; Alex M Clark; Krishna Dole; Barry A Bunin
Journal:  Drug Discov Today       Date:  2016-11-22       Impact factor: 7.851

Review 4.  The Next Era: Deep Learning in Pharmaceutical Research.

Authors:  Sean Ekins
Journal:  Pharm Res       Date:  2016-09-06       Impact factor: 4.200

5.  Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets.

Authors:  Alexandru Korotcov; Valery Tkachenko; Daniel P Russo; Sean Ekins
Journal:  Mol Pharm       Date:  2017-11-13       Impact factor: 4.939

Review 6.  Underscoring interstrain variability and the impact of growth conditions on associated antimicrobial susceptibilities in preclinical testing of novel antimicrobial drugs.

Authors:  David A Sanchez; Luis R Martinez
Journal:  Crit Rev Microbiol       Date:  2018-12-06       Impact factor: 7.624

Review 7.  Knowledge-based approaches to drug discovery for rare diseases.

Authors:  Vinicius M Alves; Daniel Korn; Vera Pervitsky; Andrew Thieme; Stephen J Capuzzi; Nancy Baker; Rada Chirkova; Sean Ekins; Eugene N Muratov; Anthony Hickey; Alexander Tropsha
Journal:  Drug Discov Today       Date:  2021-10-27       Impact factor: 8.369

8.  Bioactivity Comparison across Multiple Machine Learning Algorithms Using over 5000 Datasets for Drug Discovery.

Authors:  Thomas R Lane; Daniel H Foil; Eni Minerali; Fabio Urbina; Kimberley M Zorn; Sean Ekins
Journal:  Mol Pharm       Date:  2020-12-16       Impact factor: 4.939

9.  Collaboration for rare disease drug discovery research.

Authors:  Nadia K Litterman; Michele Rhee; David C Swinney; Sean Ekins
Journal:  F1000Res       Date:  2014-10-31

Review 10.  A brief review of recent Charcot-Marie-Tooth research and priorities.

Authors:  Sean Ekins; Nadia K Litterman; Renée J G Arnold; Robert W Burgess; Joel S Freundlich; Steven J Gray; Joseph J Higgins; Brett Langley; Dianna E Willis; Lucia Notterpek; David Pleasure; Michael W Sereda; Allison Moore
Journal:  F1000Res       Date:  2015-02-26
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