Pipelining ChemAxonPresentation by et al, Szilárd Dóránt · December 2008
This presentation gives a thorough overview about the component collection that allows you to get access to all ChemAxon tools from Pipeline Pilot. In the introduction part the basic quick facts are provided about the collection.
Full abstractThe major part of the presentation shows the development of the pipeline functionalities within ChemAxon that starts with the description of the available features. Among the most important functionalities the Standardizer, the Reactor, the Marvin applets, the MCS based clustering, the microspecies distribution, the IUPAC name and molecule converter or the burden eigenvalue descriptor are worth to mention. However the presentation puts the focus on the 2008 improvements, on the changes that happened in the versions from 1.2 to 1.4. The features that are emphasized in the presentation are as follows:
- Chemical Terms Calculator
- Canonicalization with Standardizer
- IUPAC naming components
- Changes in Reactor
- Clustering with LibMCS
- JChem Base insert
- JChem Database search
- Improved error reporting
On the closing slides of the presentation the planned components are discussed.
2008 Accelrys European User Group Meeting · 9-12 December 2008.
Download
Chemical Terms - Functions for CheminformaticsPresentation by György Pirok, Zsolt Mohácsi, Nóra Máté, József Szegezdi, István Cseh, Attila Szabó, Miklós Vargyas, Szabolcs Csepregi, Ákos Papp, Ferenc Csizmadia · June 2008
Pharmaceutical research is not just about molecules, it is about realizable molecules having certain properties. The available set of computable properties is growing, each function usually calculates a specific physicochemical parameter. These functions, like partial charge distribution, p , logD carry important chemical information, but the most interesting questions today are more complex.
Full abstractMany questions are related to ADMET. Will a planned specific compound be absorbed well, what are its major metabolites, how will it behave in a certain reaction, will it be biologically active?
Scientists need an easy way to formulate calculations by the combination of property predictions,mathematical functions, and substructure matching functions. The Chemical Terms language was developed with this purpose in mind. More than a hundred functions are currently provided, and can be extended through a public plugin interface. The evaluator engine is an integratable component, which provides instant evaluation of Chemical Terms expressions entered as text. The Chemical Terms language has been used to improve the chemical feasibility of various cheminformatics tools such as database filtering, pharmacophore screening, drug design, virtual synthesis and metabolic pathway prediction.
8th International Conference on Chemical Structures (ICCS) · June 1-5, 2008
Download
What's new for Pipeline PilotPresentation by Larry Norder, Szilárd Dóránt · March 2008
Pipeline Pilot solutions are based around a powerful client-server platform that lets you construct workflows by graphically combining components for data retrieval, filtering, analysis, and reporting. ChemAxon implemented these functionalities to a number of its products that are described in this presentation as for 2008.
Full abstractAfter the introduction of the ChemAxon’s product line the presentation starts to give an overview about the products that implemented Pipeline Pilot: Marvin Sketch, Marvin View, the Calculator Plug-ins or Chemical Terms. Among the ChemAxon tools the JChem Base is emphasized as several features and interfaces were added to that. Most of the innovations improved the searching facility of the database manager through concentrated functionality. The next important development the presentation talks about is the canonicalization functionality of the Standardizer that is simple to use but it can handle complex tasks too. The virtual synthesis of the ChemAxon’s Reactor was updated with Pipeline Pilot solutions as well to make the tool more effective, flexible, smart and compatible. The Pipeline Pilot was implemented to the Instant JChem as well to create and update databases that can be intuitively searched and analyzed. On the last few slides there’s an overview about the plan of the current and future developments, the list of the available components and the ones that are planned to become a component.
2008 SciTegic Pipeline Pilot User Group Meeting, March 5-7, 2008
Download
Chemical Terms, a Language for CheminformaticsPresentation by György Pirok, Attila Szabó, Ferenc Csizmadia, István Cseh, József Szegezdi, Miklós Vargyas, Nóra Máté, Szabolcs Csepregi, Zsolt Mohácsi · March 2007
This presentation gives an overall understanding about ChemAxon’s Chemical Terms which is a simple but extensible language, a general interface to combine chemical functions for various cheminformatics purposes. Briefly the Chemical Terms enables the software programs to extend their “chemical intelligence”.
Full abstractOn the first slides of the presentation you can read about the problems that belong to the topic of the Chemical Terms. The related questions are listed within four categories: virtual reactions, filtering, pharmacophore mapping and random evolutionary de Novo drug design. The following slides give the answers for these questions presenting the development of the Chemical Terms functionality to solve the above mentioned chemical problems. Afterwards you can read about the Chemical Terms’ function examples including substructure matching, chemical calculations, the calculation of returning molecules and combining functions in the tools. In the end of this part of the presentation the Chemical Terms Editor is introduced in a few words.
The major part of the presentation focuses on the ChemAxon applications that the Chemical Terms functionality is built in. The Instant JChem, the filters of the Pipeline Pilot, the Reactor, the Metabolizer are mentioned in this section. Finally an overview of the upcoming Chemical Terms features is discussed in three major groups: simplified syntax, simplified editing and new functionalities.
American Chemical Society Spring meeting, March 25-29th, 2007
Download
Making "Real" Molecules in Virtual SpacePresentation by György Pirok, Nóra Máté, Jenő Varga, József Szegezdi, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia · January 2006
Predicting “realistic” compounds of given chemical reactions with virtual synthesis tools usually requires the manual intervention of experienced chemists in the enumeration phase for the selection of appropriate reactants, assignment of the corresponding reaction sites, and removal of the unlikely products.
Full abstractTo automate the virtual synthesis process, we have moved the expertise intensive parts from the compound library design phase to the reaction library design phase. ChemAxon is building an in silico reaction library containing important preparative transformations, where each reaction definition contains a generic transformation scheme and additional rules to handle the various starting compounds according to the corresponding chemo-, regio-, and stereoselectivity issues. Having well designed reaction definitions in hand, our software tool is able to generate synthetically feasible compound libraries with minimal effort in the enumeration phase.
J. Chem. Inf. Model. 2006, 46, 563-568.
Download
Making real molecules in virtual spacePresentation by György Pirok, Nóra Máté, Jenő Varga, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia · March 2005
The computational description of chemical structures is a well established area. The field of synthetic chemistry, however, still does not have adequate software tools, since preparative chemistry is an experimental science full of unexpected transformations.
Full abstractThe mathematical foundation is too complicated to solve and there is no standard method to describe the valuable knowledge of experienced synthetic chemists in exact formulas, which could be evaluated by computers. In the scope of this presentation, we will introduce ChemAxon’s approach for modeling reactions, a software component able to generate synthetically feasible products and some interesting applications of this technology.
The number of known compounds is permanently growing, currently, more than 24 millions are registered in the Chemical Abstracts
1. But this is only a teeny-weeny part of the realizable molecules. The estimated number of realizable molecules is so high due to the wonderful variability of organic elements
2. Even much higher than the number of atoms in the Universe, which can be estimated from its mass
3. Our current technology does not enable us to synthesize and test most of the possible compounds in the foreseeable future, thus, we need something much faster and cheaper than preparative or combinatorial synthesis helping us to select those few molecules worth to be synthesized.
9th Annual InfoTechPharma® Conference, 15-16 March, 2005.
Download
How can generic reactions be specific? Virtual synthesis with “smart” reactions.Presentation by György Pirok, Nóra Máté, Szilárd Dóránt, Miklós Vargyas, Ferenc Csizmadia (ChemAxon) · April 2004
High throughput screening initiated a new gold-rush in drug discovery. Although the reef of combinatorial chemistry has enriched the pharmaceutical industry with many new biologically active compounds, there is a growing demand to access new molecules even before they are synthesized.
Full abstractHuge virtual libraries can be generated by computer programs, but the quality of the results depends on technology of reaction modeling. It is a hard nut to crack, since preparative chemistry is not an abstract science and theory often fails in practice.
The ideal virtual reaction library contains a few hundred generic reactions equipping chemists with classified preparative transformations. Furthermore, the ideal virtual reactions are specific to generate chemically feasible products from each individual compound. So, how can a generic reaction be specific?
227th ACS National Meeting · March 28 – April 1, 2004 · Anaheim, California
Download
Virtual synthesis with “smart” reactionsPresentation by György Pirok, Nóra Máté, Szilárd Dóránt, Miklós Vargyas, Szabolcs Csepregi, Ferenc Csizmadia · November 2003
Modeling chemical structures is a scientifically well grounded area, proving it’s self in theory as well as in practice. However, there are many traps on the road to virtual reaction processing.
Full abstractChemical Terms turn generic reaction equations to “smart” transformations. Smart transformations are generic, since they can be applied to whole compound libraries. Smart transformations are specific as well by „knowing” reactivity and selectivity rules they handle each compound specifically. Awell defined library of smart transformations can form the basis of various applications, such as virtual synthesis, retrosynthesis, fragmentation, structure canonization and metabolism analysis. Chemical Terms as a general chemical expression format, enables chemists to define complex conditional expressions in a standard format like structure queries and advanced pharmacophore point definitions.
eCheminformatics 2003, November 10-15, 2003
Download
A Novel Approach to Modeling Molecular Transformations and its Various ApplicationsPresentation by György Pirok, Nóra Máté, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia · August 2003
With the advent of high throughput screening and combinatorialchemistry computer assisted chemistry plays an important role in selecting and designing new drug candidates. Pharmaceutical R&D demands methods for transforming huge numbers of chemical structures in a reasonable time.
Full abstractModeling chemical structures is a well established approach which has proved itself in practice, however there are many hazards on the road to virtual reaction processing. Specific virtual reactions work well with specific compounds but they are not usable for batch processing large molecule libraries. On the other hand, the application of generic reaction equations needs permanent manual control to eliminate chemically meaningless or not synthesizable products.
An ideal chemical transformation rule needs to be generic to apply to compound libraries yet specific so as to be able to process only chemically feasible transformations.
Drug Discovery Technology, Boston, USA, August 10-15, 2003
Download
New Way of Mono-BOC Protection of DiaminesPresentation by László Kovács, József Szegezdi · February 2003
The calculated pKa values could serve good interpretation for the selective reaction of different diamines in acidic medium. Summarizing the basic requirement for mono protection is 5 difference between the pKa values of the two amino groups.
Full abstractThe lower is the pKa of the free amine of the mono-Boc species the higher is the yield of the mono-boc product. Isolated diamines can be reacted according to the following rule: in acidic medium the lower in neutral medium the greater pKa valued nitrogen can be protected with acceptable selectivity. Alkyl chain longer than 3 carbons reduces the favorable neighborhood effect. Over 8 pKa difference value the amines can be reacted selectively in chemical reactions.
There are certain problems which this model overlooks:
1. Stability of the protected amines vs. pH and temperature
2. Stability of the heterocyclic systems vs. pH and temperature
The bulky Boc O is very sensitive to the steric hindrance, which is confirmed by regioselectivity of the Boc-protection and the sensitivity of the reaction velocity to the steric hindrance.
Advancing Library Design and Organic Synthesis, La Jolla, California, February 24-27, 2003
Download
