The 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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Most importantly, it is prone to miss biologically relevant conformations. Representing flexible molecules on a continuous scale without the need of discrete sampling provides much higher degree of reliability and accuracy. But how can we address the complexity challenge and cope with the continuous flexibility within a manageable computational time frame?

A flexible 3D alignment method that overlays molecules by optimizing a potential function similar to the intersection of their molecular volumes has been developed. This method, based on the analytical representation of the conformational flexibility, is capable of aligning two or more chemical structures to very high accuracy. Nevertheless, the approach offers reasonable performance for drug-like molecules.

A generalization of the flexible conformational analysis apparatus enables the exploration of the entire conformational space of a molecule. The statistical analysis of this blurred spatial region provides a fairly low dimensional molecular descriptor which serves as the basis for a high throughput 3D virtual screening technique.

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The 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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Such 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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Many 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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In the first paragraph of the presentation the method of the tautomer calculation is described thoroughly. Afterwards the concept of the dominant tautomers are explained that enables to generate all tautomers of the submitted molecule even the very unstable examples that have no practical significance. This is followed by the description of the canonical tautomers that are relevant in duplication filtering during compound registration. For the deeper understanding of the ChemAxon’s tautomer generation methods the calculation of the tautomer distribution is described through several examples and even two concrete test cases are provided in the end of the presentation.

American Chemical Society Fall meeting, Aug 19-23rd, 2007
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It also has to be admitted, that these software work well, they provide good image quality, are rich in features and do not show stability or performance problems. So why implement “yet another molecular structure visualization software”?

ChemAxon already has an active chemical editor and viewer development as well as a plugin technology for property prediction. From our users and own experience we felt that none of the existing visualization tools provided all of the key features in one device and that some functionalities are not available, particularly;

• web-enabled high quality rendering
• managing very large complexes
• all types of common molecular surfaces are available
• molecular properties are mapped on surfaces
• interactive monitors and controls
• platform independent
• available as programmers toolkit (Java API)
• professional support

MarvinSpace, ChemAxon’s new 3D molecule visualization and modeling software aims to achieve a wide spectrum of functions combined with near print quality interactive rendering in a platform independent solution. MarvinSpace should be useful for content providers, online publishers, public internet databases, chemoinformatians, medicinal chemists, modelers and biochemists.

InfoTechPharma, 13 – 16 March 2006

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Our 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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JChem, 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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However, automatic, ‘batch’ processes cannot be applied on a large number of molecules if they imply human intervention. Studies, like QSAR, pharamacophore analysis, reaction prediction might need full, complete 3D information for the compounds of interest. The widespread tools used for structure determination (force-fields or quantum chemical methods) even require a complete set of initial 3D coordinates.

Our approach intends on generating globally valid set of 3D coordinates for small and medium sized molecules, based on local structural criteria. Over against iterative, backtrack based structure predicting algorithms, our method is capable of satisfying partially inconsistent requirements. Such situations are common for structures holding polycyclic, rigid details.

Goals mentioned above can be achieved using coordinates interpreted in a space with a Minkowski metric. Our coordinate assignment process is divided into the following parts: (I) Automatic generation of distance criteria based on chemically relevant local properties, such as bond stretches, bond angles, dihedral angles, etc. (II) Multi-dimensional coordinate assignment which fulfills all the criteria. (III) Geometry optimization using a force field extended to the multi-dimensional Minkowski space. The optimization eliminates the over-3D components and yields the 3D coordinates.

The Role of Chemistry in the Evolution of Molecular Medicine, Szeged, Hungary, June 27-29, 2003
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The 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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