A Summary of 2012 publications

17 Dec

I have been reviewing the publications that have been published in 2012 in collaboration with members of the RSC eScience team and other collaborators. It’s been a busy year and I am very lucky to be able to collaborate with such a group of excellent people.


Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration, S. Ekins, A.M. Clark, A.J. Williams, Molecular Informatics 31 (8), 585-597, 2012 Link

Redefining Cheminformatics with Intuitive Collaborative Mobile Apps, A.M. Clark, S. Ekins, A.J. Williams, Molecular Informatics 31 (8), 569-584, 2012 Link

Open PHACTS: Semantic interoperability for drug discovery, A.J. Williams, L. Harland, P. Groth, S. Pettifer, C. Chichester, E.L. Willighagen, Drug Discovery Today. 2012 Link

Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation, A.J. Williams, S. Ekins, V. Tkachenko, Drug discovery today, 5, 2012 Link

Disruptive Strategies for Removing Drug Discovery Bottlenecks, S. Ekins, C.L. Waller, M.P. Bradley, A.J. Williams, Nature Publishing Group, 2012 Link

Blind trials of computer-assisted structure elucidation software, A. Moser, M.E. Elyashberg, A.J. Williams, K.A. Blinov, J.C. DiMartino, Journal of Cheminformatics, 4(5), 2012 Link

Elucidating ‘undecipherable’ chemical structures using computer‐assisted structure elucidation approaches, M. Elyashberg, K. Blinov, S. Molodtsov, A.J. Williams, Magnetic Resonance in Chemistry, Volume 50(1), 22–27, 2012 Link

Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models, A.J. Williams, J. Wilbanks and S. Ekins, PLOS Computational Biology, 8(9), e1002706, 2012 Link

Applying Linked Data Approaches to Pharmacology: Architectural Decisions and Implementation, A.J.G. Gray, P. Groth, A. Loizou, S. Askjaer, C. Brenninkmeijer, K. Burger, C. Chichester, C.T. Evelo, C. Goble, L. Harland, S. Pettifer, M. Thompson, A. Waagmeester, A.J. Williams Link

Annotating Human P‐Glycoprotein Bioassay Data, B.Zdrazil, M. Pinto, P. Vasanthanathan, A.J. Williams, L. Zander Balderud, O. Engkvist, C. Chichester, A. Hersey, J.P Overington, G.F. Ecker, Molecular Informatics, 31(8), 599-609, 2012 Link

Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision., C. Brenninkmeijer, C. Evelo, C. Goble, A.J.G. Gray, P. Groth, S. Pettifer, R. Stevens, A. J. Williams, E. Willighagen, Proceedings of 2nd International Workshop on Linked Science 2012—Tackling Big Data, December 2012

Four disruptive strategies for removing drug discovery bottleneck, S. Ekins, C.L. Waller, M.P. Bradley, A.M. Clarke and A.J. Williams, Link

A Combined Atomic Force Microscopy and Computational Approach for the Structural Elucidation of Breitfussin A and B: Highly Modified Halogenated Dipeptides from Thuiaria breitfussi, K.Ø. Hanssen, B. Schuler, A.J. Williams, T.B. Demissie, E. Hansen, J.H. Andersen, J. Svenson, K. Blinov, M. Repisky, F. Mohn, G. Meyer, J-S. Svendsen, K. Ruud, M.E. Elyashberg, L. Gross, M. Jaspars, and J. Isaksson, Link

Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates, C. Southan, A.J. Williams and S. Ekins, Drug Discovery Today,

Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses, S. Ekins, A.M.Clark and A.J. Williams, ACS Green Chemistry (publication accepted)



Automated Systematic Nomenclature Generation for Organic Compounds by Andrey Yerin and Antony J. Williams, Wiley Interdisciplinary Reviews of Computational Molecular Science. LINK

Ligand-Based Modeling of Toxicity, Sean Ekins, Sandhya Kortagere, Matthew Krasowski, Antony J. Williams, Jim Xu, and Michael Zientek, Chapter 12, Drug Design Strategies: Quantitative Approaches LINK

Accessing, Using and Creating Chemical Property Databases For Computational Toxicology Modeling, Antony J. Williams, Sean Ekins, Ola Spjuth and Egon L. Willighagen, Published as a chapter in Computational Toxicology, Methods in Molecular Biology series, Humana Press, USA (Clifton, NJ), 929, 221, 2012 LINK

A. Day, A.J. Williams, C. Batchelor, R. Kidd and V. Tkachenko Utilizing Open Source Software to Facilitate Communication of Chemistry at RSC, Published in Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond (Woodhead Publishing Series in Biomedicine), Editors: Lee Harland and Mark Forster LINK


About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database ( Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (, a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service ( and the RSC lead for the PharmaSea project ( attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
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Posted by on December 17, 2012 in Publications and Presentations


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