You will find a range of scientific and technical resources presented or written by both ChemAxon staff and our users. The page contains a number of presentations, articles, animations, videos and other media files about ChemAxon’s softwares. On the bottom of the page you can browse among our ten most recent featured presentations.
You may need AcrobatReader or PowerPointViewer to read our presentations. Some of the following articles are linked to Journal publications and you may need subscription to access the full text.
Sections:
Scientific Presentations: This section of the library contains a complete list of scientific articles and presentations made by ChemAxon. If you want to get a general, overall understanding of our products this section will be rather useful for you. Please notice there is also a breakdown according to product.
Scientific and Technical Product Presentations: This page lists the presentations that focus on the key features and capabilities of each product from a technical or scientific point of view. This section is suggested to the advanced users of ChemAxon who want to get a deeper understanding of our softwares.
User Presentations: Talking all the time about ourselves is boring and less genuine. Please browse among the presentations of our users: what are they use the ChemAxon softwares for? Why did they decide being our customers? How did they migrate from a previous system and what are their experiences about working with ChemAxon? Within this section among many ChemAxon users you’ll find references from companies like GlaxoSmithKline, Pfizer, Thomson Reuters, Abbott Laboratories, Eli Lilly, AstraZeneca, Novartis or Takeda.
Archive of ChemAxon’s User Group Meetings: The User Group Meetings (UGM) are always the most important platforms to meet with us. Currently the ChemAxon organises two meetings in a year: one in Europe and one in the United States. This section tries to give a taste of ChemAxon’s UGMs: besides the formal presentations and posters along with abstracts you’ll find photos on the Gallery tab that reflects the spirit of the meeting.
Media: This section contains videos about presentations, webinars and animations. These resources are the easiest and fastest way to get a deeper understanding of our products.
In Press: Stories, articles featuring ChemAxon in press.
Reference Space was defined by collecting known PDE inhibitors (“seeds”) from available literature and databases, and its property space was determined by applying the Lipinski and Veber parameters using InstantJChem. The searchable Chemical Space was composed by the recent edition of the 10 major vendor databases (cca. 10 M compounds). The ligand-based 2D similarity search (InstantJChem) was performed by setting a similarity treshhold (0.65-0.7 Tanimoto). The resulting set was shrinked to match the “reference property space” applying the appropriate physico-chemical parameter ranges. The filtered focused library was further analyzed to reach a reasonable diversity („seed” compound representation/ chemotype distribution) using InstantJChem and LibMCS and the process was completed by visual inspection. In the presentation we discuss our experience in the focused library generation and share the lessons we learnt during the application of the ChemAxon software family. This work was partially supported by the National Development Agency (NKÜ) grant: #KMOP 1.1.1-07/1-2008-0029) [1] Decornez H, Gulyás-Forró A, Papp A, Szabó M, Sármay G, Hajdú I, Cseh S, Dormán G, Kitchen DB Design, selection, and evaluation of a general kinase-focused library. ChemMedChem. 4(8), 1273-8 (2009). [2] A. Tovar, H. Eckert, J. Bajorath, Comparison of 2D Fingerprint Methods for Multiple-Template Similarity Searching on Compound Activity Classes of Increasing Structural Diversity, ChemMedChem, 2, 208-217 (2007).
Both fragment counts and pharmacophore pattern fingerprints are classical, well-established molecular descriptors, thought to be complementary. The former provide a molecular skeleton-dependent encoding of the main substructures, while the latter capture information about relative spatial distributions of pharmacophore groups and are less focused on how these are interconnected (thus prone to successful lead hopping). We now set to explore hybrid intermediates of these two extreme classes of descriptors, such as pharmacophore fragments (substructures of the pharmacophore feature-colored molecular graph, having atom symbols replaced by their types) – all while benefitting from the pH-dependent flagging scheme achievable by means of the ChemAxon microspecies calculator. Alternatively, atom coloring by their partial charge, using the ChemAxon charge plugin, will be explored. Examples of usage of these descriptors in QSAR and similarity searches will be shown.
Kinases are now one of the most intensely pursued classes of drug targets with approximately 30 distinct kinase targets and over 200 kinase inhibitors in clinical development. Keeping up with all published kinase structure activity information is a daunting, but necessary task for all researchers in the field. With the explosive growth of mobile computing environments, including the iPhone, Android-based devices, and the soon to be released iPad, it has become important for scientific software companies to enable technology and content access on these ubiquitous devices. We will present a major enhancement to our previously released iKinase iPhone application. This enhancement enables structure-based searching into our Kinase Knowledgebase on iPhone/iPod/iPad devices using ChemAxon structure-search technology.
Thomson Reuters has been indexing chemistry in patents for Derwent World Patents Index since before the development of commercial structure search engines. This paper will discuss the challenges of indexing specific and Markush entities from patents; how the development of new technologies has impacted chemical patent searching over time and, in particular, how recent developments are re-invigorating the Markush space, opening up the potential of “end-user” Markush searching and the development of new tools for understanding and using the “patent space” especially in drug development.
Pyxis Discovery provides Cheminformatics-based lead discovery services to companies that are active in small molecule drug discovery. Our approach for designing and selecting screening compound libraries is based on the principles of leadlikeness and facilitates a rapid and efficient lead discovery process. Recently, Pyxis Discovery has launched Chemonaut, a compound sourcing platform which enables search and procurement from more than 50 vendor catalogues. This talk will provide an insight into data and structure standardization and filtering procedures implemented for creation and maintenance of the Chemonaut database using both ChemAxon tools and in-house developed algorithms.
We will describe the “fun” we are having creating rules and workflows to tidy up the data from chemical supplier catalogues for our compound sourcing database.
In an increasingly information rich research environment, drug discovery scientists need a robust and easy to use way to exchange information, knowledge and decisions with colleagues. Pfizer’s answer to these collaboration issues has been to make extensive use of Microsoft SharePoint and OneNote as our project team collaboration platform of choice. Collectively known inside the company as “OnePoint”, the increasing use of these technologies across all phases of discovery has yielded significant benefits in terms of productivity and co-operative working. However, as useful as these tools are in a generic business context, there still remains some progress to be made extending them for more specific scientific uses. This presentation aims to outline what that progression might look like for chemistry centric users within the Microsoft SharePoint environment, and stimulate thoughts and discussion.
SkunkWerks used JChem to provide substructure and similarity searches across an existing Screening Library System. The solution was integrated with the existing RIA applications and SkunkWerks proprietary back end. SkunkWerks opted for JChem’s Web Services as the means to communicate with JChem Base. Using JChem’s Web Services SkunkWerks was able to seamlessly integrate substructure/similarity searches into the application. This session will present the solution that was developed using JChem and Flex (Adobe Flex) for a RIA implementation.
This talk will follow-on to the presentation given by Brett Hiemenz at the 2009 US UGM which described the uses of a Service Oriented Architecture (SOA) and the problems faced in a mixed technology environment. During 2009 and 2010 IT has undergone a push to simplify the architecture, technologies and vendors used in order to reduce the cost of on-going support and maintenance of our vast application portfolio. One solution has been to consolidate the number of vendors used and standardise of a range of webservices that can provide the required functionality. ChemAxon was chosen to provide a number of these generic chemistry functions used by Discovery IT ranging from structural searching to 2D rendering. We will begin by discussing how the ChemAxon toolkit and cartridge has been integrated into the enterprise environment and detail the effort required to migrate from some existing vendors to ChemAxon. We will also discuss the advantage SOA has played in this migration with respect to cost and client applications. Finally, we will show details of how the ChemAxon product has evolved in our systems and led to gains in consistency and supportability.
