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Articles & Reports
CSAT Newsletter Issue 18
People and PlacesCongratulations to Trustee David Wild and his wife Sue on the arrival of twins, Alina Marie and Alexis Anne, on August 21 2008, sisters for Nathan and Emma.
Sue Cardinal, co-chair of the CINF education committee of the ACS Division of Chemical Information, gave birth to an 8 pound 2 ounce baby boy, Torstan, on September 13 2008.
Nancy Lambert, former senior information analyst at ChevronTexaco, has received the 2008 International Patent Information (IPI) Award. Nancy has spent more than 30 years in the chemical industry, becoming a leading authority in chemical and polymer patent searching. She was also recognised for her ongoing support of and active participation in the Patent Information Users Group (PIUG), of which she is a founding member. Chemistry Central has appointed Jan Kuras as Associate Publisher to develop new Open Access journals in chemistry.
Jan Velterop, Springer’s director of Open Access, and a driving force behind Springer Open Choice, has left Springer to pursue a new career as CEO of KnewCo. He joined Springer in August 2005 from BioMed Central.
Derek Debe has won the ACS COMP paradigm shift award, sponsored by Open Eye.
Neil Kipling, founder and CEO of IDBS has been awarded an honorary doctorate (DUniv) from the University of Surrey.
Carmen Nitsche has been appointed as the VP of the content group at Symyx Software.
Eric Jamois has been VP, sales and marketing at BioDiscovery since April 2008. Rita Wilby has been senior director, business development at Assay Depot since February 2008.
David Hughes, formerly of MDL, is working on research into self-assembling copolymers at the University of Basel, Switzerland.
We are sad to report the following deaths:
Kevin Haraki died from liver cancer, on January 24 2008, aged 59. An obituary appeared in the June 2 issue of C&EN. His industrial research career began at Lederle (now Wyeth) in 1979. He retired in 2005.
Mike Corkill, an account manager at the STN Agency in Cambridge, died in a road accident on March 27 2008. An obituary appeared in the May 2008 issue of RSC News. Call for Nominations: ACS Division of Chemical Information (CINF) 2010 Herman Skolnik AwardThe ACS Division of Chemical Information established this Award to recognise outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honour of the first recipient, Herman Skolnik.
By this Award, the Division of Chemical Information is committed to encouraging the continuing preparation, dissemination and advancement of chemical information science and related disciplines through individual and team efforts. Examples of such advancement include, but are not limited to, the following:
The Award consists of a $3000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. In recent years, the Award Symposium has been organised by the recipient.
Nominations for the Herman Skolnik Award should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Nominations and supporting material should be sent by e-mail to Phil McHale at philmchale@comcast.net. Paper submissions are no longer acceptable. The deadline for nominations for the 2010 Herman Skolnik Award is June 1 2009. Guenter Grethe, CINF Awards Chair Yvonne Martin wins 2009 Herman Skolnik AwardYvonne Connolly Martin, retired Senior Volwiler Research Fellow at Abbott Laboratories, is the recipient of the 2009 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). Details about the award are given on Page 2 along with the Call for Nominations for the 2010 award.
Yvonne Martin has been at the forefront of cheminformatics throughout her professional career which was spent entirely at Abbott Laboratories. She has been a founder and constant driving force in the development and use of computational chemistry and its application to computer aided drug discovery. Her studies in QSAR, molecular diversity, molecular graphics, pharmacophore analysis, molecular similarity and combinatorial chemistry have had a great impact the work of theoretical and experimental medicinal chemists. Her overall contributions have helped shape the modern definition of drug discovery. While she developed many methods and supervised their implementation, she never limited herself to a single method or application for solving real-world problems. She finds great pleasure in sharing her work with any interested researchers.
Yvonne has authored or co-authored more then 60 peer-reviewed papers, about 40 book chapters, and more than 20 reviews. Additionally, she edited 6 books and 7 patents were issued in her name. These publications and her numerous presentations at national and international meetings provided important insights into computational drug discovery. She has served on many journal editorial boards and NIH study sections. For her many contributions to the field of molecular modelling, Yvonne has received several awards and honours including the Accomplishment Award from the Society for Biomolecular Sciences.
Yvonne Martin received a BA in Chemistry in 1958 from Carleton College and a PhD in Chemistry in 1964 from Northwestern University. She started her career in 1958 as Research Assistant at Abbott Laboratories and, moving through the ranks, retired in 2006 as Senior Volwiler Research Fellow. In 1967-1968, she spent a sabbatical year at Pomona College with Professor Corwin Hansch, which made her an early proponent of QSAR. Yvonne was one of the founders of the International QSAR Society (now called Cheminformatics and QSAR Society) in 1989 and served as its Chair in 2001-2005. Yvonne is highly respected by all of her colleagues worldwide and this award is a well-deserved recognition of an outstanding research career. Guenter Grethe, Chair, CINF Awards Committee 2008 CINF Meritorious Service Award to Bill TownCSA Trustee Bill Town has been awarded the ACS CINF Meritorious Service Award. This award is given to members who made outstanding contributions to the division. This is only the seventh time this award has been given in the history of the division. Bill’s involvement in divisional activities started with being a member of the Publication Committee (1993–1996). As member of the Program Committee (1989–1992 and 1996–1998), his interest was primarily on the program level, organising symposia and speaking at many technical sessions at national meetings of the ACS. At the recent ACS meeting in New Orleans, held jointly with the American Institute of Chemical Engineers (AIChE), he co-organised four sessions on the topic ‘Engineering the Transition to Bioeconomy’.
In recent times, Bill took on a more active role in governance. He is currently an Alternate Councillor (2006–2008), and he has served the Division as Chair-Elect (1999), Chair (2000), and Past-Chair (2001). In addition, he chaired the Awards Committee (2002–2005) and the Nominating Committee (2001). Bill’s continued and varied contributions and strong commitment to CINF are of great benefit to the division. A Practical Introduction to ChemoinformaticsThe aim of this short course held by the Department of Information Studies at the University of Sheffield is to provide a broad introduction to chemoinformatics.
Through the generous support of the CSA Trust and the Molecular Graphics and Modelling Society (MGMS), two student bursaries were awarded to Claire Speight, from the School of Pharmacy and Chemistry, Liverpool John Moores University in the UK, and Laura Guasch, from the Department of Biochemistry and Biotechnology at Rovira & Virgili University, Tarragona, Spain. They report from an intense but enjoyable three days in Sheffield in June.
The topic of this course is closely related to the methodology used in my own research. I am doing my PhD thesis in the Nutrigenomics Research Group at the Biochemistry and Biotechnology Department of the Rovira & Virgili University, in Tarragona, Spain. My main goal is to identify novel PPARg (peroxisome proliferator-activated receptor-gamma) agonists from natural products through pharmacophore modelling and QSAR analysis. Although it was a introductory course, it ranged over the whole field of chemoinformatics from combinatorial libraries to structure-based drug design. I valued the fact that there were practical sessions, since this has enabled me to learn new programs and through them to solve chemoinformatic problems.
I found the session ‘Molecular Diversity and Compound Selection’ particularly interesting, as I intend to use these methodologies with my ligands, to try to distinguish between different ligands of PPAR (agonists, antagonists, alpha, beta/delta, gamma, duals, pan) through information of descriptors. Ideally, I would like to obtain a cluster for each class of ligand.
I also enjoyed learning about workflows and software that allows the design of a sequence of operations which are executed one after another.
Another topic of great interest was structure-based drug design. In particular, I am interested in how ligands bind into the active site using approaches for molecular docking. The practical session of this part consisted of docking three molecules into the binding cavity of a protein to determine which molecule is the correct ligand. In my own work, I am planning to dock ligands extracted from libraries of natural products, with the aim of identifying compunds that act as agonists.
Also of interest to me was the session ‘Pharmacophore Generation’, as this is an area in which I have already have some experience; however, I was able to understand the limitations of current methods better and discuss with the tutors the problems that I find.
Other aspects that I valued were the organisation of the course; in my opinion, this was excellent and very well coordinated. I was able to interact with the other participants of the course and to get to know their research. Although the group was small, there were people of various disciplines, which made it more interesting to learn how the techniques can be used to solve different problems. This course has given me the opportunity to learn new techniques which I hope to apply in my own research. It provided an opportunity for me to get new ideas, to learn best practice and to gain software experience to maximise productivity in my own drug discovery research activities.
Laura Guasch
This chemoinfomatics course has been consistently over-booked throughout its history, and this year was no exception. Of the 19 lucky attendees, there was a wide range of people from both industry and academia. Several fields were represented, including bioinformatics, drug design and toxicology. Some had chemistry backgrounds, and wanted to learn about the informatics side; others were computer programmers wanting to learn about tthe chemistry; a few people came simply to learn as much as they could about both. This diversity of backgrounds gave the team at Sheffield the very difficult task of covering many areas of chemoinformatics, in just three days! This may perhaps explain why the course required a very intense structure.
The course material was taught using a combination of lectures, practical classes and group work. The group work was a running topic for discussion over the first two days, culminating in a 15 minute presentation on the topic. This enabled the groups to start discussions on the first evening (which also allowed everyone to become acquainted), and then add to their presentations as the course continued.
The lectures and practical sessions were divided into nine sessions to cover all relevant areas of chemoinformatics, including database searching, diversity and compound selection, QSAR and pharmacophore generation. The lectures were well presented and the practical classes were easy to follow, considering that most people on the course met at least one new piece of software, and there were a few who had never even used SMILES before. The whole group was able to proceed at the same pace however, due to the excellent help from the course tutors.
All of this hard work was well rewarded, however. Each evening ended with a fine three-course meal at some of the best restaurants in and around Sheffield. An excellent blend of work and play! These social outings were a brilliant opportunity to talk to fellow attendees, to find out how the course could be useful to them, and also to network in general. All three evenings were very much enjoyed by everyone.
The course gave all attendees the opportunity to learn the basics of many areas of chemoinformatics, without the need to apply for a full qualification in the subject. This is unlike anything else which is currently available. The expertise of the lecturing staff provided an excellent working environment. From a personal perspective, I had the opportunity to try methods I would not normally use in my own research group. I also gained an insight into how the tools we use for toxicity prediction are used differently for chemical screening and drug design.
Overall, the general feeling was that the course equipped one with the basic knowledge needed to go on and investigate further. Although the course was intense, all participants agreed that nothing should be removed. The course contains all relevant areas of chemoinformatics without being overwhelming. It achieves its goals well, and it is of little surprise that it is over-booked every year.
Claire Speight Maciej Haranczyk receives the Jacques-Émile Dubois Grant for 2008Maciej Haranczyk, a graduate student at the Univeristy of Gdansk, has been awarded the CSA Trust Jacques-Émile Dubois Grant for 2008. The grant program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. Maciej has used the grant to support a six week research visit to the chemoinformatics group in the Department of Information Studies at the University of Sheffield in the UK. The aim of the visit was to familiarise himself with the techniques that are required for processing large chemical datasets.
‘I have had to extend my area of expertise in order to proceed with the main theme of my research – the development of combinatorial chemistry methods based on quantum chemical evaluation of chemical properties,’ Maciej explains, ‘with the hope that I will be able to deliver an automated system that can be used in the advanced design of molecules and materials.’
The research involves two steps:
i) the combinatorial generation of libraries of molecular structures ii) the screening of the libraries for the targeted molecular property using quantum mechanical methods.
At each step of development of the method, various chemoinformatics tools and techniques are required, the most important being chemical structure representation and storage, along with diversity analysis and other approaches to analyse different chemical spaces. Maciej chose the Sheffield Chemoinformatics group as the place to gain experience in these areas and to continue carrying out this research project.
During his time in the Sheffield group, Maciej worked with John Holliday and Peter Willett. The project focused on the evaluation of different fingerprint representations and similarity measures for similarity searching for typical database screening applications. The results of these investigations are about to be submitted for publication as a regular research article.
Maciej believes that the benefits of the visit are more than just publishable results. ‘The period I have spent in Sheffield was a stimulating experience’ Maciej says, ‘Sheffield’s group provides an excellent research environment with expertise from friendly group members and open discussions. Every day I could learn new things and better understand the problems we are facing in the field of chemical information. I am sure the knowledge I am gaining over these few weeks will be useful in my future career.’
Living in a foreign city can be also an interesting social experience, as Maciej found. ‘Sheffield is a very pleasant place to live. The people are nice and helpful. The city seems to be a modern, safe and exciting without having all the drawbacks of other big cities such as being too expensive or too crowded. It is conveniently located next to the beautiful Peak District, where you can hike during the weekends. It has everything except the good weather, although when it is sunny, it’s beautiful!’
Maciej has recently obtained a doctoral degree, and is about to join the Lawrence Berkeley National Laboratory in Berkeley, California, as the recipient of the 2008 Glenn T. Seaborg postdoctoral fellowship. He will continue his research efforts in the area of chemoinformatics and computational chemistry. Information and Knowledge Management in the International Pharmaceutical Industry: 50th Annual General Meeting of the P-D-R 2008The Pharma Documentation Ring (P-D-R) held its 50th Annual General Meeting (AGM) in Montreux, Switzerland from the 23rd – 26th September 2008. This year’s meeting celebrated the 50th anniversary of the group’s founding. The P-D-R is an association whose members represent the scientific information departments of the leading international R&D-based pharmaceutical corporations. There were two new corporate members (Ferring Pharmaceuticals and UCB) added during the previous 12 months. The 23 member companies continue to account for approximately 60% of the total global turnover of ethical drugs (approximately $500 billion); by far the majority of the top 20 global pharmaceutical companies are P-D-R members.
Forty delegates attended this year’s meeting, which was hosted by Novartis. The 50th anniversary event included a half day meeting to which former P-D-R members and 12 information vendors were invited. Henning P. Nielsen (Novo Nordisk), current President of the P-D-R, and Alexander Mullen, past President, opened the meeting with an amusing look backwards on the past decades of the P-D-R. The following keynote speakers were decidedly future facing.
Jeff Elton, COO and Head of Strategy at Novartis Institute for Biomedical Research, Inc., spoke about informatics and innovation in drug discovery. Matthias Horx, founder of the Zukunftsinstitut and one of the most influential futurists in the German-speaking world, gave a thought provoking talk on scientific futurology and mega-trends in society. Philipp Karmires presented Google’s view on innovations after ten years of business. Brief presentations by each of the vendors followed, including Chemical Abstracts Service, Ebsco Information Services, Elsevier B.V., FIZ Karlsruhe, Georg Thieme Verlag, Informa, Nature Publishing Group, Springer, Swets, Thomson Reuters, Wiley-Blackwell, and Wolters Kluwer. They shared their vision of the information future supported by a poster session.
A principal highlight of this meeting was the strategic topic session which focused on the future information world and how this should be reflected in the different topic groups where P-D-R members work together. The results of a P-D-R internal survey on the vision of the future integrated information world, first conducted in 2003 and repeated now, five years later, were summarized, and then the groups invited all participants in a poster session to exchange views and to set expectations for the future work.
Each of the topic groups organized a portion of the agenda which highlighted areas of interest within that group. A theme which emerged at this year’s meeting within several groups was text mining. The Chemical and Patent Information group highlighted approaches for chemical entity recognition and the new technologies available to offer enhanced ways of searching, analyzing and processing text. The Biomedical Information team presented text mining in biomedical content from the perspective of an information professional highlighting the different tools and approaches needed for text mining vs. traditional searching. The Business Intelligence topic group focussed on creating value in the business areas of the pharmaceutical industry through text mining. The various uses for text mining approaches were described and how text mining can fill the time gap to avoid the issue of “information aging”, but is not yet at a place where it can replace manual curation by experts The final presentation with a text mining theme was from the Technology team about the added value of semantic technologies and what is missing.
Information and Knowledge Management presentations included several case studies around Web 2.0 approaches. The Library Affairs and Copyright team gave an update on the outcomes of the special meeting held earlier this year which brought publishers, intermediaries, and copyright agencies together to discuss the issues facing pharmaceutical companies in the provision of information.
An ongoing feature of the P-D-R AGM is the review of information-related developments within the member companies over the previous twelve months. Common themes that emerged were the use of SharePoint as an enterprise platform, the increasing use of Web 2.0 features as wikis and blogs, continued outsourcing of non-core information activities, the continuous need for internal marketing, and ongoing organizational changes.
The 51st P-D-R AGM will be held in Leesburg, Virginia from the 22nd - 25th September 2009 and will be hosted by Bristol-Myers Squibb and Merck & Co.
The P-D-R web site can be found at http://www.p-d-r.com. This item did not appear in the printed version of the CSAT Newsletter
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