Markush structures – From molecules towards patents 2009 ICIC presentationPresentation by Szabolcs Csepregi, Nóra Máté, Róbert Wagner, Szilárd Dóránt, Erika Biró, Tamás Csizmadia, Tim Dudgeon, Ferenc Csizmadia · October 2009
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent applications for the description of compound classes.
Full abstractThe presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and larger repeating units, position and homology variation). It will be shown how Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space searched without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).
The presentation will focus on the most recent developments (position variation, repeating units, homology variation), and further developments will be discussed towards full patent handling.
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Representation, searching & enumeration of Markush structures - from molecules towards patents - 2009 updatePresentation by Erika Biró, Ferenc Csizmadia, Nóra Máté, Róbert Wagner, Szabolcs Csepregi, Szilárd Dóránt, Tamás Csizmadia · August 2009
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent applications for the description of compound classes.
Full abstractThe presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and larger repeating units, position and homology variation). It will be shown how Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space searched without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).
The presentation will focus on the most recent developments (position variation, repeating units, homology variation), and further developments will be discussed towards full patent handling.
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Structural Search Using ChemAxon ToolsJanuary 2009
Structural searching techniques are invaluable tools in all cheminformatics systems including but not limited to rational drug design, compound registration systems and laboratory information management systems.
Full abstractJChem, one of ChemAxon’s major suites of programs, provides a very rich set of features related to structural searches. These features are demonstrated by examples. Covered topics are: substructure, exact, superstructure, MCS (maximum common substructure) and similarity searching. Reaction and R-group searches (including R-logic) are also available, which are complemented by a rich set of query features. SMARTS and query features of the MDL formats are supported.
The database components of JChem are also described: JChem Base and JChem Cartridge for Oracle. An example of a fast MCS-based clustering is also presented.
Finally the recently developed descriptive Chemical Terms Language is demonstrated by powerful structural searches.
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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.
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Migration from ISIS environmentsPresentation by et al, Szabolcs Csepregi · November 2008
The presentation focuses on the differences, similarities, pros and contras of migration from an ISIS environment to a related ChemAxon product. It gives a proper overview about the features of several ChemAxon products, it describes the functionalities of the ISIS tools, you can find independent comparisons, migration case studies and feedback from users and an appendix about the technical resources of ChemAxon products.
Full abstractThe presentation starts with a brief overview of ChemAxon tools like the Marvin family, the Calculator plugins, the Chemical naming, the JChem family, the Markush features, the Standardizer, the drug discovery tools and even the embedded ChemAxon tools.
The first product that is discussed in this presentation is JChem Cartridge. This part starts with the thorough overview of the software’s purpose, features, operators and functions. Afterwards the migration from MDL/Direct cartridge and from ISIS/Host is described through independent comparison and from technical point of view. On the end of this section an overview of a migration questionnaire takes place.
In the next section the ChemAxon’s Standardizer goes through a comparison against the Cheshire including such topics like counting groups, adding explicit hydrogens, group conversion and structure checker.
In the following slides the Instant JChem is compared to the ISIS/Base with special focus on architecture, databases, forms and security. Within the topic of the migration the presentations gives an overview about the comparison of the JChem’s Data Tree and the ISIS Hview and the migration options are explained here thoroughly.
Afterwards comes the brief description of the JChem for Excel and its short comparison to ISIS for Excel. It is followed by the migration of the custom applications including Java applications, .NET applications, web based applications and SOAP.
Finally among the ChemAxon products the migration of the Web Services is discussed.
The presentation closes with the review of the developers’ resources emphasizing the Java API, the Marvin Applets for web applications, the .NET API and native .NET solutions, SOAP interface, AJAX GUI and the integration of ChemAxon components to vendors’ softwares.
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ChemAxon for DevelopersPresentation by Ferenc Csizmadia · November 2008
The presentation aims to give an overall understanding of the ChemAxon’s application programming interfaces, graphical user interfaces, additional development informations mostly about Instant JChem and the company’s softwares’ integration.
Full abstractThe main topics of the presentation are as follows:
- Java API
- Marvin Applets for web applications
- .NET API over JNBridge
- Native .NET solution
- JChem Cartridge for Oracle
- SOAP interface
- AJAX GUI
The final slide of the presentation gives an overview about the software vendors that integrated ChemAxon softwares. For example the Pipeline Pilot, KNIME, Spotfire, Aureus and Integrity are mentioned among the most important vendors.
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Alternatives to MDL® CheshirePresentation by György Pirok · November 2008
The presentation gives a thorough comparison of MDL’s Cheshire and ChemAxon’s tools. Among the alternatives of the Cheshire the presentation lists three ChemAxon functionalities: the Java API, the Chemical Terms and the Standardizer.
Full abstractIn the first few slides the three previously mentioned tools are described. Afterwards the Cheshire, the Java API and the Standardizer is compared to each other from three different point of view:
- Counting Groups
- Adding explicit hydrogens
- Group conversion
In the end of the presentation stands as a summary of the comparison that Java API provides similar flexibility for programmers as Cheshire, though it is a widely used language. The Chemical Terms feature can handle Cheshire codes in the same complexity level but the Chemical Terms expressions can be used in other cheminformatics applications. The Standardizer enables chemists to create conversion rules without encoding.
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Working with IUPAC names using ChemAxon toolsPresentation by Daniel Bonniot de Ruisselet, Veréb Rita, Miklós Vargyas · August 2008
Chemical names constitute a widely used and convenient way to characterize compounds. Historically, useful compounds have been assigned common names, like toluene. Systematic ways to assign names to all compounds have later been developed and standardized by the International Union of Pure andApplied Chemistry (IUPAC).
Full abstractSuch systematic names reveal the presence of characteristic groups, like carboxylic acids and classes of compounds, like esters. Currently, IUPAC is designing precise rules to assign a unique preferred name to each compound, which can be useful, for instance, in the context of patents.
ChemAxon provides tools to generate names from structures, and to generate structures from names. In both cases, we strive to support both traditional and preferred IUPACnames.
236th ACS National Meeting & Exposition · August 17-21, 2008
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Representation, searching and enumeration of Markush structures - from molecules towards patentsPresentation by Szabolcs Csepregi, Nóra Máté, Szilárd Dóránt, Erika Biró, , Tim Dudgeon, Ferenc Csizmadia · June 2008
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent chemical patent applications for the description of compound classes.
Full abstractThe presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and position variation). It will be shown how Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space searched without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).
The presentation will focus on the most recent developments, and further developments will be discussed towards full patent handling.
8th International Conference on Chemical Structures (ICCS) · June 1-5, 2008
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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
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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
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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
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JChem Cartridge: Cheminformatics Platform for OraclePresentation by Péter Kovács, Szilárd Dóránt, Szabolcs Csepregi, Nóra Máté, György Pirok, Ferenc Csizmadia · March 2006
JChem Cartridge adds chemical knowledge to the Oracle platform. Data can be searched by structure, substructure and similarity criteria through extending Oracle’s native SQL language. Chemical data can be easily inserted and modified using SQL.
Full abstractJChem Cartridge relies on Oracle’s extensible indexing framework for best search performance. In order to take advantage of this capability, the index type has to be applied.
InfoTechPharma, 13 – 16 March 2006
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3D structure prediction and conformational analysisPresentation by Gábor Imre, Ödön Farkas · June 2005
Numerous theoretical method in the field of computational chemistry falls back on the availability of 3D structural information about compounds. Determining molecular structure without human interaction is an essential component of several techniques, like QSAR, 3D pharmacophore analysis, reaction prediction, etc. Current computational tools used for structure determination including force-fields and quantum chemical methods, even require a complete set of initial 3D coordinates. The efficiency of 3D structure based HTS tools also can be enhanced by employing conformational analysis to yield multiple valid structures.
Full abstractOur approach utilize a composition of several methods ranging from pure rule based multi dimensional distance geometry method to data based stored substructure lookup features in a flexible software framework. The actual implementation is a highly portable JAVA software, which fits a broad scale of applications: it is used in small web drawing applets as well as standalone database processing component.
The coordinate determination process can be best characterized by the “divide and conquer” approach: the structure is composed of fragments, which are joined together. From the available fragment conformers the conformers of the joined structures can be generated during the fusing step. The fragment conformers are generated either through further fragmentation or with an elemental structure/conformer prediction method, consequently the conformational analysis is an inherent part of the building process. The novelty of our approach lies in the diversity of utilized such elemental methods and the arisen scalability options.
7th International Conference on Chemical Structures, 5-9 June 2005
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Advanced Structural Search Using ChemAxon ToolsPresentation by Szabolcs Csepregi, Szilárd Dóránt, Nóra Máté, Miklós Vargyas, Péter Kovács, György Pirok, Ferenc Csizmadia (ChemAxon) · March 2005
Molecular search techniques are invaluable tools in all cheminformatics systems including rational drug design, compound registration systems and laboratory information management systems. Often they provide a basis for more complex applications like functional group identification, bond cleavage, virtual reaction processing, standardization, toxic fragment identification, etc.
Full abstractJChem, one of ChemAxon’s major suites of programs, provides a very rich set of features related to structural search which is described in this presentation from different points of view: interfaces and options, database solutions, formats and platforms, the performance of the JChem Base. The Oracle was extended to support chemical database operations through JChem Cartridge for Oracle which has got two examples in this presentation: SQL examples and SQL examples using Chemical Terms. The JChem tools can handle a wide variety of query features that are detailed below:
- Atom query features
- Query of SMARTS atoms
- Bond and fragment query features
- E/Z double bond stereo searching
- Tetrahedral Chirality
- Reaction search
- R-group search
- Explicit and implicit hydrogens
- Canonicalization
ChemAxon’s JChem suite contains a broad range of chemical search facilities with a rich set of features besides the above mentioned ones. The final part of the presentation gives a proper overview about the Chemical Terms language, the Similarity search, the Maximum Common Subgraph and R-group decomposition. All the tools mentioned in this presentation are 2005 releases and built 100% on Java platform.
9th Annual InfoTechPharma® Conference, 15-16 March, 2005.
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Advanced Structural Search Using ChemAxon ToolsPresentation by Szabolcs Csepregi, Szilárd Dóránt, Nóra Máté, Miklós Vargyas, Péter Kovács, György Pirok, Ferenc Csizmadia · November 2004
The molecular search techniques represent an extremely wide range of solutions in all cheminformatics systems. This presentation starts with highlighting some crucial examples of applications: compound registration, database search, pharmacophoric group identification, functional group identification, cleavage bond identification, virtual reaction procession, standardization, toxical fragment identification.
Full abstractJChem, one of ChemAxon’s major suites of programs, provides a very rich set of features divided into two major groups: one is atom by atom search (ABAS) or structural search, the other is similarity search. The following slides describe the structural search in the ChemAxon’s JChem Base. The Oracle was extended to support chemical database operations through JChem Cartridge for Oracle which has got examples about using substructure and similarity searches and Chemical Terms examples. The JChem tools can handle a wide variety of query features that are detailed below:
- Atomic features
- Atomic SMARTS features
- Bond and components features
- Double bond stereo search
- Tetrahedral chirality stereo search
- Reaction search
- R-group search
- Hydrogens
Afterwards you can read about the functionalities that are related to the structural search: Standardizer, similarity search, R-group decomposition and pairs of molecules. Among these tools the Chemical Terms is emphasized in this presentation. The new Chemical Terms language is a beneficial complement to structural searches allowing data mining made easy.
Applications of Cheminformatics and Chemical Modelling to Drug Discovery, 8-19 November 2004
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JChem: Java Applets and Modules Supporting Chemical Database Handling from Web BrowsersPresentation by Ferenc Csizmadia · March 2000
A Java based development tool for building portable chemical information systems is presented. The system contains applets for constructing web-based interfaces and classes that add structure handling to relational databases. Custom applications built with JChem can combine SQL and structural queries.
Journal of Chemical Information and Computer Sciences, Volume 40, Issue 2 (March 27, 2000), Pages 323-324
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A New Format for the Efficient Storage of Molecular StructuresPresentation by Péter Csizmadia, Ferenc Csizmadia · August 1999
The presentation looks for the answers regarding new, efficient storage of molecular structures. The pdf file gives a short summary about the problem itself, it gathers the possible solutions and in the end of the presentation it will suggest one.
Full abstractThe internet is too slow to handle a large number of molecules in a minimum available time. The problem won’t be solved if the molecular data is stored in a standard format or in some proprietary binary format. The major solution that is introduced in this presentation is the compressed molfiles or csmole files. The second part of the presentation focuses on the searching in a network chemical database with the solutions of ChemAxon’s softwares that can import and export csmol files (MarvinSketch, MarvinView and JChem).
The 5th International Conference on Chemical Structures (5th ICCS), Noordwijkerhout, June 6-10, 1999
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Java Applets and Modules Supporting Chemical Database Handling from Web BrowsersPresentation by Ferenc Csizmadia · June 1999
A Java based development tool for building portable chemical information systems is presented. The system contains applets for constructing web-based interfaces and classes that add structure handling to relational databases. Custom applications built with JChem can combine SQL and structural queries.
The 5th International Conference on Chemical Structures (5th ICCS), Noordwijkerhout, June 6-10, 1999
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The Development of a Web Based System for the Online Shopping of CompoundsPresentation by Ferenc Csizmadia, Ferenc Darvas · June 1999
This presentation describes the role of the complex chemical web applications through the example of the Chemazon, a webshop of a large amount of compounds produced by the ComGenex.
Full abstractIn the introduction the complex chemical web application’s technology is described: it combines the elements of web technology, database technology and chemical software technology. The complexity of the problem requires new directions from the ChemAxon: creating Java based softwares. It is compatible with almost all operation systems, web servers and database servers too.
The 5th International Conference on Chemical Structures (5th ICCS), Noordwijkerhout, June 6-10, 1999
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