Medicinal Chemistry App from RSC goes live on iTunes

Today I received notification that an app to accompany a forthcoming RSC book ” The Handbook of Medicinal Chemistry: Principles and Practice” went live on iTunes.

“The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, we developed otherwise difficult-to-access tools in a portable format for use in meetings, on the move and in the lab. The app is optimised for iPad and contains calculator functions designed to ease the process of calculating values of: Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding.

If you have an iPad then you can download the app from here.

The book itself will be published in November 2014 and will provide a comprehensive, everyday resource for a practicing medicinal chemist throughout the drug development process

The app will be updated on an ongoing basis with new algorithms and calculators so make sure you check back or update when it tells you.

MedChemToolkit

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Presentations given at the ACS Meeting in San Francisco #ACSsanfran

Recently returned from the ACS meeting in San Francisco it was a busy and very successful conference. We presented to a number of different divisions on a lot of our activities and many of our collaborators presented also. The list of talks is below and as more links become available I will update this page. What I learned is that we need to present in MANY other divisions other than CINF…the attendees of the CHED and ANLY divisions for sure were interested in what we have to say. We will do more of this…

Applying Royal Society of Chemistry cheminformatics skills to support the PharmaSEA project, A.J. Williams. A. Pshenichnov, V. Tkachenko, K. Karapetyan and D. Sharpe, ACS Fall Meeting, San Francisco, August 2014 Link

How the InChI identifier is used to underpin our online chemistry databases at the Royal Society of Chemistry, A.J. Williams, V. Tkachenko and K. Karapetyan, ACS Fall Meeting, San Francisco, August 2014 (Invited Talk) Link

Dealing with the complex challenge of managing diverse chemistry data online, A.J. Williams, A. Pshenichnov, V. Tkachenko and K. Karapetyan, ACS Fall Meeting, San Francisco, August 2014 Link

Encouraging undergraduate students to participate as authors of scientific publications, A.J. Williams, ACS Fall Meeting, San Francisco, August 2014 Link

Who knew I would get here from there: How I became the ChemConnector, A.J. Williams, ACS Fall Meeting, San Francisco, August 2014 (Invited Talk) Link

Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project, A.J. Williams. A. Pshenichnov, J. Steele, C. Batchelor, V. Tkachenko, K. Karapetyan and V. Tkachenko, ACS Fall Meeting, San Francisco, August 2014 Link

Using an online database of chemical compounds for the purpose of structure identification, A.J. Williams, A. Pshenichnov and V. Tkachenko, ACS Fall Meeting, San Francisco, August 2014

The Royal Society of Chemistry and its adoption of semantic web technologies for chemistry at the epoch of a federated world, A.J. Williams and V. Tkachenko, ACS Fall Meeting, San Francisco, August 2014 Link

Accessing 3D printable chemical structures online. V. F. Scalfani, A. J. Williams, R. M. Hanson, J. E. Bara, A. Day, V. Tkachenko, ACS Fall Meeting, San Francisco, August 2014 Link

Using the BRAIN, biorelations and intelligence network, for knowledge discovery. A. Mons, B. Mons, A. Krol, A.Baak, A.J. Williams, V. Tkachenko, ACS Fall Meeting, San Francisco, August 2014

Navigating chemistry requirements for data management and electronic notebooks: A case study. L. R. McEwen, A. J. Williams, V. Tkachenko, J. G. Frey, S. J. Coles, A. E. Day, C. Willoughby, W. R. Dichtel, ACS Fall Meeting, San Francisco, August 2014

The Chemical Analysis Metadata Platform (ChAMP): Thoughts and Ideas on the Semantic Identification of Analytical Metrics, S. Chalk,  A.J. Williams, V.Tkachenko San Francisco, August 2014 Link

Integrating Jmol/JSpecView into the Eureka Research Workbench. S. Chalk, M. Morse, I. Hurst, A.J. Williams, V.Tkachenko, A. Pshenichnov, R. Hanson, ACS Fall Meeting, San Francisco, August 2014

Clustering the Royal Society of Chemistry chemical repository to enable enhanced navigation across millions of chemicals. K. Karapetyan, V. Tkachenko, A. J. Williams, O. Kohlbacher, P. Thiel, ACS Fall Meeting, San Francisco, August 2014 Link

Experiences and adventures with noSQL and its applications to cheminformatics data. V. Tkachenko, A.J. Williams, K. Karapetyan, A. Pshenichnov, M. Rybalkin, ACS Fall Meeting, San Francisco, August 2014 Link

Faculty profiling and searching in the Eureka Research Workbench using VIVO and ScientistsDB. S. Chalk, M.Morse, I. Hurst, A.J. Williams, V. Tkachenko, A. Pshenichnov, ACS Fall Meeting, San Francisco, August 2014

Supporting the exploding dimensions of the chemical sciences via global networking. V. Tkachenko, A.J. Williams, S. Vatsadze, ACS Fall Meeting, San Francisco, August 2014 Link

Toward extracting analytical science metrics from the RSC archives. S. Chalk, A.J. Williams, V. Tkachenko, C.Batchelor, ACS Fall Meeting, San Francisco, August 2014

Dereplication applications for computer-assisted structure elucidation (CASE) and the ChemSpider database. P.Wheeler, A. Moser, J. DiMartio, M. Elyashberg, K. Blinov, S. Molodstov, A.J. Williams, ACS Fall Meeting, San Francisco, August 2014 (Invited  talk)

Real structures for real natural products − really getting them right and getting them faster. P. Wheeler, A.J. Williams, M. Elyashberg, R. Pol, A. Moser, ACS Fall Meeting, San Francisco, August 2014

The increasing importance of chemical information literacy in the life of graduate students: Contributions from the ACS Division of Chemical Information (CINF, G. Baysinger, J. Currano, J. Garritano, L. R McEwen, A. J Williams

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Using an online database of chemical compounds for the purpose of structure identification #ACSsanfran

Using an online database of chemical compounds for the purpose of structure identification

Online databases can be used for the purposes of structure identification. The Royal Society of Chemistry provides access to an online database containing tens of millions of compounds and this has been shown to be a very effective platform for the development of tools for structure identification. Since in many cases an unknown to an investigator is known in the chemical literature or reference database, these “known unknowns” are commonly available now on aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. Searching by elemental composition is the preferred approach as it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results can be refined by appropriate filtering to identify the compounds. We will report on integrated filtering and search approaches on our aggregated compound database for the purpose of structure identification and review our progress in using the platform for natural product dereplication purposes.

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Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project at #ACSsanfran

This is my presentation on Thursday 14th August at the ACS Meeting in San Francisco

Open innovation and chemistry data management contributions from the Royal Society of Chemistry resulting from the Open PHACTS project

The Royal Society of Chemistry was pleased to contribute to the Open PHACTS project, a 3 year project funded by the Innovative Medicines Initiative fund from the European Union. For three years we developed our existing platforms, created new and innovative widgets and data platforms to handle chemistry data, extended existing chemistry ontologies and embraced the semantic web open standards. As a result RSC served as the centralized chemistry data hub for the project. With the conclusion of the Open PHACTS project we will report on our experiences resulting from our participation in the project and provide an overview of what tools, capabilities and data have been released into the community as a result of our participation and how this may influence future projects. This will include the Open PHACTS open chemistry data dump including the chemistry related data in chemistry and semantic web consumable formats as well as some of the resulting chemistry software released to the community. The Open PHACTS project resulted in significant contributions to the chemistry community as well as the supporting pharmaceutical companies and biomedical community.

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Accessing 3D Printable Chemical Structures Online at #ACSsanfran

This presentation was given by Vincent Scalfani and covers the work we have done to provide access to 3D printable chemical structures online…

Accessing 3D Printable Chemical Structures Online

We have been exploring routes to create 3D printable chemical structure files (.WRL and .STL). These digital 3D files can be generated directly from crystallographic information files (.CIF) using a variety of software packages such as Jmol. After proper conversion to the .STL (or .WRL) file format, the chemical structures can be fabricated into tangible plastic models using 3D printers. This technique can theoretically be used for any molecular or solid structure. Researchers and educators are no longer limited to building models via traditional piecewise plastic model kits. As such, 3D printed molecular models have tremendous value for teaching and research. As the number of available 3D printable structures continues to grow, there is a need for a robust chemical database to store these files. This presentation will discuss our efforts to incorporate 3D printable chemical structures within the Royal Society of Chemistry’s online compound database.

 

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Who knew I would get here from there and how I became the ChemConnector. #ACSsanfran

This was my fifth talk at the ACS meeting in San Francisco…..

Who knew I would get here from there. How I became the ChemConnector.

As the ChemConnector and one of the people responsible for creating ChemSpider I have become well known in the chemical information world. I get to connect with some of the brightest minds in the domain, have participated in meetings with Microsoft, Google, various government institutions and with some of the top chemical and pharmaceutical companies. While my path to this point feels at some times like a random walk, and certainly I never set a trajectory to become a chemical information specialist as I am a spectroscopist by training, I look back upon my career with a lot of satisfaction. We are now at a time when information is becoming so important to support and guide the discovery process. At the same time the opportunity to communicate your science to the masses is upon us. I will discuss how I became the ChemConnector, my Twitter handle, and why I believe entering the field of cheminformatics at this time holds incredible potential for influence.

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Dealing with the Complex Challenge of Managing Diverse Chemistry Data Online to Enable Chemistry Across the World #ACSsanfran

This is my third presentation today at the ACS meeting in San Francisco on 11th August 2014

Dealing with the Complex Challenge of Managing Diverse Chemistry Data Online to Enable Chemistry Across the World

The Royal Society of Chemistry has provided access to data associated with millions of chemical compounds via our ChemSpider database for over 5 years. During this period the richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process of implementing a new architecture to build a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on how our efforts to manage chemistry related data has impacted chemists and projects across the world and will review specifically our contributions to projects involving natural products for collaborators in Brazil and China, for the Open Source Drug Discovery project in India, and our collaborations with scientists in Russia.

 

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Teaching analytical spectroscopy using online spectroscopic data #ACSsanfran

My first talk of three on August 11th 2014 at the ACS San Francisco meeting

Teaching analytical spectroscopy using online spectroscopic data

The teaching of spectroscopy can be a complex and challenging task. The Royal Society of Chemistry has been developing online resources for a number of years that provide access to analytical data as well as interactive quizzes and challenge sets. The RSC data repository houses over 250,000 spectra at this time including mass spectrometry, NMR and IR data and these are utilized to provide online games to test students capabilities, to underpin the SpectraSchool  training website and to produce source data for students and teachers alike to use in their teaching and self-training efforts. This presentation will provide an overview of RSC resources that can be used to teach spectroscopy using our online data and tools.

 

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Encouraging students to start publishing early in their career #ACSsanfran

My second talk of three on August 11th 2014 at the ACS Meeting in San Francisco.

Encouraging students to start publishing early in their career

Many students spend enormous amounts of their time engaged with their computers, accepting of course that mobile devices are simply computers of a different form factor. Engaged with the social networks, utilizing computer platforms to source and share content of various forms, their contributions of “data” into what is the cloud, and in many cases a void, is enormous. What community and career benefit might result from those students spending some of their time contributing chemistry related data to the world? What challenges lie in the way of their participation and how might participating have a positive, or negative impact on their future career. The Royal Society of Chemistry hosts a number of chemistry data platforms to which students can actively contribute and for which their participation can be measured. Moreover the RSC’s micropublishing platform allows chemists to learn how to write up their scientific work, obtain review from their peers and chemistry professors in a non-threatening environment and produce an online published work in less than day that is both citable and available as a shared resource for the community. This presentation will demonstrate how to participate and encourage engagement from students early in their education. There are no longer any technology barriers to the sharing of the majority of chemistry related data.

 

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How the InChI identifier is used to underpin our online chemistry databases at the Royal Society of Chemistry #ACSsanfran

This is my presentation at the ACS San Francisco Fall Meeting on August 10th 2014

How the InChI identifier is used to underpin our online chemistry databases at the Royal Society of Chemistry

The Royal Society of Chemistry hosts a growing collection of online chemistry content. For much of our work the InChI identifier is an important component underpinning our projects. This enables the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a platform encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.

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