2006 UGM Archive

ChemAxon b124dd5f17

09-05-2006 12:06:27

This is the scientific presentation list ordered according to user or ChemAxon affiliation and presentation sequence.

If visitors would like to forward questions to authors please send an email to aa_at_chemaxon.hu and I can forward to the author.

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ChemAxon b124dd5f17

09-05-2006 12:09:16

Wednesday June 7th

Title: ChemAxon products’ role in ACE Organic, a Web-based organic chemistry homework program

Author: Robert B. Grossman

Institution: University of Kentucky

Abstract: ACE Organic is a Web-based organic chemistry homework program that offers feedback specific to a student’s particular response to a question. Students draw their response with MarvinSketch, and it is analyzed with JChem methods in order to determine the most appropriate feedback to provide.

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ChemAxon b124dd5f17

09-05-2006 12:26:39

Title: Integrating JChem and Marvin into the Integrity® drug discovery and development portal

Authors: Rosa Alentorn, Gerard Chiva and Ann Wescott*

Institution: Prous Science

Abstract: The pharmaceutical industry must track chemical structure information throughout the drug discovery, development and marketing life cycle. Prous Science provides a variety of services to assist industry in this endeavor, and has incorporated the ChemAxon JChem cartridge and Marvin applications into several of these. We describe some of the challenges faced with incorporating these tools into an existing product and how they were met, as well as future developments envisaged.

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ChemAxon b124dd5f17

09-05-2006 12:32:24

Title: The widespread deployment of JChem integrated applications at Evotec

Author: Alistair Sedwell

Institution: Evotec

Abstract: This presentation will demonstrate the wide variety of in-house developed applications that utilise Chemaxon tools at Evotec. The talk includes an overview of the Chemaxon tools we currently use, how we use them, how they are integrated into our applications, and what we plan to do in the future. The problems that have been encountered during this work and the associated solutions will be discussed. The presentation will conclude by focusing on our medicinal chemistry workbench application known as Esma, and demonstrate how useful drug design tools based on the JChem libraries can easily be delivered to the chemist's desktop.

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ChemAxon b124dd5f17

09-05-2006 12:34:15

Title: BeeHive - a system for storage and retrieval of research data

Author: Mats Dahlberg

Institutions: iNovacia - Biovitrum

Abstract: When Biovitrum was spun out from Pharmacia Corp in 2001 we urgently needed a new system for storing biological and chemical data for the entire R&D organisation. It has become an efficient tool through which all data are readily available for analysis by all scientists and project teams. Structures and arbitrary assay data columns can be freely combined, and complex queries can be saved and shared between users.

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ChemAxon b124dd5f17

09-05-2006 12:36:10

Title: A Virtual Atlas Of Click Chemistry: The Space Of Cheap And Easy Molecules

Author: Maneesh Yadav

Institution: The Scripps Research Institute

Abstract: The "click chemistry" philosophy proposed by Sharpless et al. can be succinctly described as synthetic route construction with an emphasis on the use of "easy" reactions, i.e. those with predictably high, context-independent exergonicities. What the quantitative statistical differences between the set of molecules accessible via click synthetic routes, and other relevant subsets of synthetically accessible molecules are, remains an open question. We are using ChemAxon’s tools to generate a virtual library of molecules that can be constructed using only click reactions in a small number of synthetic steps. By constraining our starting material pool to high production volume chemicals and using only click reactions, we hope to generate a virtually exhaustive set of "cheap and easy" molecules. The aim is to use the library to predict the distributions of properties and medicinal activities from molecules that should be "process" ready. Practical details about our methods for reaction specification and running ChemAxon’s tools on a parallel cluster will also be described.

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ChemAxon b124dd5f17

09-05-2006 12:37:49

Title: Instant JChem

Author: Tim Dudgeon

Institutions: Informatics Matters/ChemAxon

Abstract: Recognising the need many customers have for simple out of the box JChem and Marvin based solutions for managing compound, assay and inventory data, we are creating an end user application designed around these needs. The initial Instant JChem module that will be demonstrated is aimed around creating, editing and managing JChem databases, and for analysing their contents by querying and sorting the data. Plans for future modules that extend these capabilities, will also be described.

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ChemAxon b124dd5f17

09-05-2006 13:27:38

Title: HTS follow-up using JChem Base; virtual and vendor neighbors.

Author: James Baxendale

Institution: Synaptic Science

Abstract: There is always intense pressure to move rapidly from 'hits' in a primary screen to optimization on validated leads. In this, informatics personnel need to worry, not just about presenting screening data in a useful way (using clustering for example), but framing those hits in the context of literature compounds, identifying related commercially-available compounds, and capturing and organizing the plethora of follow-up ideas from chemists. In particular, the unique challenges posed by the management of virtual and commercial compound databases with several million entries has lead us to design and implementation heuristics that facilitate the rapid, dynamically tunable identification of compounds using substructure, 'lead-like' and chemical filters. For the medicinal chemists on the project team, following-up HTS hits is an opportunity to think creatively. Tracking and sharing chemists' ideas (virtual compounds) and commercially-available compounds, interactively filling SAR gaps with those same compounds and visualizing project data in a multiplexed fashion are techniques we will discuss in this talk for encouraging that creativity.

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ChemAxon b124dd5f17

09-05-2006 13:33:45

Thursday June 8th

Title: Development of High-Content Molecular Libraries for Filling the Gap between Target and Ligand Chemical Spaces.

Authors: Mireille Krier*, Guillaume Bret, Nicolas Foata, Esther Kellenberger, Pascal Muller, Claire Schalon, Jean-Sébastien Surgand and Didier Rognan

Institutions: Université Louis Pasteur / CNRS

Abstract: The recent application of chemoproteomics to rational drug design requires the development of information-rich databases enabling the cross-talk between the two worlds of Ligand and Target spaces. We herewith report several in-house generated datasets which could foster an integrated chemoproteomic approach to ligand design (i) a library of 1.8 million commercially available drug-like compounds ('Bioinfo') already set-up for in silico screening, (ii) a library of 21,400 non-redundant molecular scaffolds ('SBI') generated from the Bioinfo Library, (iii) a collection of 6450 druggable active sites ('sc-PDB') from the Protein DataBank, (iv) a chemoproteomic database applied to human G Protein coupled receptors ('hGPCR-Lig') relying on precise information about 369 human GPCRs and 17,000 GPCR ligands, allowing to prioritize either scaffolds/ligands for user-defined receptors/subfamilies and vice-versa.

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ChemAxon b124dd5f17

09-05-2006 13:44:19

Title: pH-dependent Topological Fuzzy Pharmacophore Triplets.

Author: Dragos Horvath

Institution: CNRS

Abstract: This presentation introduces a novel tricentric pharmacophore descriptor – topological (2D) Fuzzy Pharmacophore Triplets, 2D-FPT, featuring several key improvements with respect to state-of-the-art pharmacophore fingerprints:pKa-dependent, -fuzzy pharmacophore feature detection.- fuzzy mapping of molecular triplets onto the basis set of pharmacophore triplets.-a novel similarity scoring scheme, accounting for simultaneously populated, simultaneously absent and differently populated triplets in molecule pairs.-The 2D-FPT monitor the population of topological pharmacophore triplets in molecules, with the number of interposed bonds serving as the measure of distance between the features. The original fuzzy pharmacophore feature assignment procedure reported here, relying on the predicted populations of ionized species at pH=7.4, has proven a better strategy than classical rule-based classification of functional groups into pharmacophore categories. It allows the 2D-FPT-based similarity score to correctly explain many unexpected activity differences observed between structurally almost identical compound pairs, thus assumed to be close neighbors by classical similarity scores. Moreover, this original 2D-FPT similarity scoring scheme (classical dissimilarity metrics failed to work with such high-dimension sparse fingerprints!) was shown to display excellent Neighborhood Behavior, outperforming 2D or 3D two-point pharmacophore descriptors or chemical fingerprints. The key innovation it features relies on the acknowledgment that simultaneous absence of a triplet in both molecules is a less constraining indicator of similarity than its simultaneous presence. Neighborhood Behavior benchmarking studies were conducted with respect to activity profile similarities of drug and reference molecules of the BioPrint® database. On this occasion, a novel metric of the similarity of two experimental activity profiles has been introduced. 2D-FPT were also successfully validated in active analog retrieval experiments from seeded compound collections. The 2D-FPT calculator was developed using the chemoinformatics developer's toolkit of ChemAxon (www.chemaxon.com)

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ChemAxon b124dd5f17

09-05-2006 13:50:58

Title: ChemAxon’s Chemical Fingerprints-Based Clustering to Assess AurSCOPE Databases Chemical Diversity.

Author: Ismail Ijjaali

Institution: Aureus Pharma

Abstract: Among the knowledge databases developed at Aureus Pharma, AurSCOPE Kinase and AurSCOPE Ion Channels are focused on drugs described as kinase inhibitors or ion channel blockers, openers or activators. Both chemical and biological data are structured into a unique knowledge management system where chemical structures of ligands as well as precise description of their targets and biological activities have been collected from published articles and patents.

The present work is aimed to assess the chemical and biological diversity of both databases. A specific query was constructed to retrieve most active non-peptide ligands. 2D molecular descriptors were computed and their distributions analyzed. Afterward, to encode the chemical space for the whole active dataset (9897 and 8371 molecules for ion channels and kinases, respectively), ChemAxon’s chemical hashed fingerprints were generated and optimized. These fingerprints were then employed to cluster these datasets using Jarp algorithm as implemented in JKlustor module. Clusters and singletons distributions at different similarity thresholds were analyzed and linked to corresponding biological activity. The findings show how highly structured databases combined with ChemAxon solutions can be an efficient tool to assist and inspire medicinal chemists, biologists, and computational chemists involved in a drug discovery project.

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ChemAxon b124dd5f17

09-05-2006 13:52:52

Title: Pipelining ChemAxon

Author: Ton van Daelen

Institution: SciTegic

Abstract: Pipeline Pilot is the industry leading enterprise platform for the automation of scientific workflows. It is designed to be open and extensible and following a fruitful joint development program between SciTegic and ChemAxon, a suite of components are now available that allow the power of the ChemAxon tools to be used within the data pipelining environment. In particular we have taken advantage of the sophisticated chemical representation of both products, and their Java APIs to produce a tight integration. In this talk we will demonstrate a number of components and discuss their implementation details, ChemAxon property calculators and structure manipulators are integrated using the Java APIs to send each molecule to the calculators and to set the return property values on the Pipeline Pilot data record. Components include property calculations, molecular ionization, molecular standardization and microspecies calculation, JChemBase integration uses the Java API to automate searching and data upload. JChemCartridge. ODBC integration components use Pipeline Pilot to generate the SQL needed to automate search and upload functions. Marvin Sketcher. Pipeline Pilot Webport, an interactive web client for end user access to protocols, takes advantage of Marvin to allow chemists to input queries graphically for upload and processing within protocols. Integration with Pipeline Pilot allows for the automation of tasks that use the ChemAxon technology. Sophisticated applications can be built by using the ChemAxon technology together with SciTegic’s cheminformatics, bioinformatics, text analysis and reporting capabilities and all the capabilities of SciTegic’s 20+ other software partners in a single workflow.

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ChemAxon b124dd5f17

09-05-2006 13:56:08

Title: Getting the most from ChemAxon and InforSense

Author: Bruno Cherel

Institution: InforSense

Abstract: During the research process, scientists require easy access to specific data sources such as Chemistry data stored in a JChem data cartridge, various vertical applications including advanced chemical calculators and tools like the Marvin Drawing tool, as well as flexible and intuitive analytical and visualization tools. InforSense KDE with ChemSense leverages the power of ChemAxon to provide a powerful environment which makes the integration of data and tools easy. In order to give scientists the ability to address complex problems using pre-built or 'build on the fly' workflows that are reusable and flexible, we investigate the use of a number of ChemAxon components used in InforSense ChemSense. We will show how easy it is to construct meaningful workflows connecting ChemAxon functionality with other components relevant in the field of Cheminformaic research. Using a series of workflow examples, we highlight the use of ChemAxon tools to accomplish tasks such as creating vendor collections from SDF files, R-group decomposition as well as library design. Throughout these examples, the use of the ChemAxon JChem cartridge and Marvin tools make it possible for these tasks to be completed with ease.

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ChemAxon b124dd5f17

09-05-2006 13:57:43

Title: Modelling experiments using Teranode XDA and ChemAxon

Author: Andrew Lemon

Institution: The Edge Software Consultancy Ltd / Teranode

Abstract: Managing experimentation from across discovery requires information systems that can deal with heterogeneous data collected from various disciplines. Each research area requires its own ontology and demands domain specific data processing and analysis. The traditional approach to this problem is to generate multiple applications. We will present our experience of integrating Chemaxon components with the Teranode XDA platform in order to build models for a variety of scientific domains from target validation to preclinical testing. We will discuss the goal of addressing the needs of multiple laboratories with standardised experiment manage platform with components for chemical processing. This will be of interest to scientists and IT professionals supporting data capture and analysis in scientific laboratories.

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ChemAxon 0815c054e1

13-06-2006 16:03:01

ChemAxon Presentation

Wednesday June 7th


Author: Alex Allardyce

Institution: ChemAxon

Abstract: Welcome

ChemAxon 0815c054e1

13-06-2006 16:17:00

ChemAxon Presentation

Title: Marvin- What`s new

Author: Szilveszter Juhos

Institution: ChemAxon

Abstract:The most important new features implemeted in Marvin and the Marvin API since the last UGM will presented. Main topics will be:

New GUI features (atom set customization, styles and multipage documents, 3D improvements, new bond, Rgroup and abbreviated group features)

File IO features (new supported file types and seeking)

Some parts of the new API

Short introduction to new plug-ins

ChemAxon 0815c054e1

13-06-2006 16:23:59

ChemAxon Presentation

Title: Structure based predictions - new Plugins

Author: Zsolt Mohacsi, Jozsef Szegezdi

Institution: ChemAxon

Abstract:This presentation demonstrates the new calculator plugins developed during the last year:

- tautomer, resonant structure, and stereoisomer generation,

- conformer generation, molecular dynamics,

- molecular surface area and geometrical property calculations.

We also present some new features to make working with calculator plugins easier. Using MarvinSpace to display plugin results will be introduced and an example illustrating how simple is to include this feature in your application will be also presented.

ChemAxon 0815c054e1

13-06-2006 16:27:15

ChemAxon Presentation

Title: Structure visualization with MarvinSpace

Author: Judit Papp, Miklos Vargyas

Institution: ChemAxon

Abstract:Overview the main features of MarvinSpace:

- representation of molecules

- molecular surfaces

- surface coloring by property mapping

- handling complexes and ligand environments

- secondary structure representation

- pharmacophore visualization

- future plans



ChemAxon 0815c054e1

13-06-2006 16:29:38

ChemAxon Workshop Presentation

Title: Conformer Generation

Author: Odon Farkas

Institution: ChemAxon, Eötvös Loránd University Budapest

Abstract:Numerous theoretical methods 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.

Our approach utilize a composition of several methods ranging from pure rule based (as classified in [3]) multi dimensional distance geometry method (described in [1]) 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 (available at [2]) as well as standalone database processing component. The coordinate/conformer generation process uses the Dreiding force field for energy calculations. Geometry structure optimization and molecular dynamics calculations are also implemented.

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 (in contrast with methods proceeds from 3D initial structures like [4]). The novelty of our approach lies in the diversity of utilized such elemental methods and the arisen scalability options.


[1] G. Imre, G. Veress, A. Volford and Ö. Farkas, ”Molecules from the Minkowski Space: An approach to building 3D molecular structures”, J. Mol. Struct. (Theochem), 666-667, 51-59 (2003)

[2] http://www.chemaxon.com/marvin

[3] J. Sadowski and J. Gasteiger, “From Atoms and Bonds to Three-Dimensional Atomic Coordinates: Automatic Model Builders”, Chem. Rev., 93, 2567-2581 (1993)

[4] J. Weiser, M. C. Holthausen, L. Fitjer, .HUNTER: “A Conformational Search Program for Acyclic to Polycyclic Molecules with Special Emphasis on Stereochemistry”, J. Comput. Chem., 18, 1265-1281 (1997)

ChemAxon 0815c054e1

13-06-2006 16:32:54

ChemAxon Workshop Presentation

Title: Power search

Author: Szabolcs Csepregi

Institution: ChemAxon

Abstract:Power search: How to tune search for efficiency and performance

Search parameters to fine-tune matching

- Search types

- Parameters to allow stricter or more loose matching

Selected Examples

- Usage of key query features/query drawing

- Chemical Terms

How to search efficiently

- Fingerprint parameters and tuning.

- What info can the fingerprint use from a query?

Matching outside a database: graphs and tricks

- isMatching, findFirst, findNext, FindAll

- Pre-matching

- Order sensitive hits

ChemAxon 0815c054e1

13-06-2006 16:35:45

ChemAxon Workshop Presentation

Title: Working with Marvin

Author: Peter Csizmadia, Tamas Vertse, Szilveszter Juhos

Institution: ChemAxon

Abstract:During this workshop we want to give a gentle introduction into the

class hierarchy of core Marvin/MarvinBeans classes and show

their usage. Practice topics (with programming examples) covered will


- How to insert new items into the Marvin menu.

- How to listen the molecule change event.

- How to handle huge files with the Marvin Beans API (the new file

seek feature).

ChemAxon 0815c054e1

13-06-2006 16:36:58

ChemAxon Workshop Presentation

Title: Working with and implementing your own Calculator Plugins

Author: Zsolt Mohacsi, Nora Mate

Institution: ChemAxon

Abstract:We are presenting a JSP application accessing Calculator Plugins. Plugins with parametrization are specified in a dynamically extendable HTML table. Input molecules are loaded through a MarvinView applet. Calculation results are presented in a result HTML table, result molecules are shown in separate pages in MarvinView or MarvinSpace.

ChemAxon 0815c054e1

13-06-2006 16:37:50

ChemAxon Presentation

Thursday June 8th

Title: Introducing the Standardizer GUI

Author: Gyorgy Pirok

Institution: ChemAxon

Abstract:A chemical compound can be represented in various ways. Therefore the canonicalization of the original structures is usually unavoidable before storing the library in a database or using in cheminformatics applications. To automate this process, ChemAxon has developed a software tool for the batch standardization of molecules according to a user defined configuration. Apart from the visualization issues (cleaning the layout, reorientation of wedges, changing the display mode of hydrogens and aromaticity, etc.), Standardizer helps in the canonicalization of mesomers and tautomers, and allows the removal of counterions or solvents, manipulation of the stereo information, sgroups, attached data, and the custom transformation of functional groups. Standardizer is integrated with the JChem database systems including the JChem Cartridge eliminating many common traps of chemical database administration.

ChemAxon 0815c054e1

13-06-2006 16:39:14

ChemAxon Presentation

Title: Introducing, what will be, the Reactor GUI

Author: Gyorgy Pirok

Institution: ChemAxon

Abstract:ChemAxon's Reactor technology was well accepted by the cheminformatics experts, but the flexible API and the command line interfaces are not too handy for chemists who are experienced with Windows or Mac applications only and in lack of programming skills or Unix expertise. Thus, ChemAxon started to develop a wizard-like user interface for Reactor bringing virtual synthesis to hands of wet chemists at the laboratory desks. The presentation gives a first view of the application including live demonstration.

ChemAxon 0815c054e1

13-06-2006 16:40:07

ChemAxon Presentation

Title: What`s new in JKlustor, LibMCS

Author: Miklos Vargyas

Institution: ChemAxon

Abstract:his workshop discusses the novel clustering technique, the maximum common substructure (MCS) based hierarchical clustering available in the JKlustor tool.

The concept of the MCS and its variants is introduced along with the analysis of the complexity of the MCS problem. Common approaches to finding the MCS of two structures are discussed and compared.

The approach taken in ChemAxon's clustering tool, LibMCS, is elaborated, including the description of the datastructures and algorithms applied.

Problems emerging in MCS based clustering are studied; strategies and heuristics applied in LibMCS are outlined.

Among various potential application areas the analysis of VHTS screens is presented.

Future development of LibMCS and JKlustor is discussed, and the workshop is finished by an open discussion when the audience can suggest further features, different strategies, applications etc.

ChemAxon 0815c054e1

13-06-2006 16:40:40

ChemAxon Presentation

Title: Oracle Cartridge latest

Author: Peter Kovacs

Institution: ChemAxon


- simplified upgrade procedure

- support for granting privileges to users in a semi-automated configuragable way


- multiple query structures can be specified to a single search operator with implicit UNION operations between the result sets.

- delayed index update with regular structure tables


- jc_evaluation_x and jc_evaluationb_x added to enable generation of tautomers, resonants....

- haltOnBadStructures option added to jc_insert

- jc_compare_vb for VARCHAR2 targets and BLOB queries (easier to handle in sqlplus)


- Empty smiles

- jc_insert function supports SDF and RDF tags

- jc_react supports synthesis codes

ChemAxon 0815c054e1

13-06-2006 16:41:20

ChemAxon Workshop Presentation

Title: Scientific Workshop,Virtual Library Generation

Author: Gyorgy Pirok

Institution: ChemAxon

Abstract:Reactor is the primary engine for virtual reaction processing, but it is less known, that the professional edition contains higher level tools for various molecule transformation tasks. Participants of the workshop will see a detailed demonstration of a multistep combinatorial synthesis including on-the-fly compound filtering and will learn ChemAxon's future plans in the field of virtual synthesis.

ChemAxon 0815c054e1

13-06-2006 16:42:05

ChemAxon Workshop Presentation

Title: Maximum Common Substructure

Author: Mikos Vargyas

Institution: ChemAxon

Abstract:Preliminary topics

1. Theory

- MCS, MCES, MOS, complexity

- approaches to find MCS

- ChemAxon's approach, comparison

2. MCS based clustering

- why

- problems

- how, speed issues, memory issues

- hierarchical vs. non-hieracrhical

3. Applications of libmcs

- effect of parameters

- worked example, combined with optimized virtual screening

- gui usage, api

4. Future

- near future, features

- long term plans, further application areas

- brain storming: what else, better ways

ChemAxon 0815c054e1

13-06-2006 16:42:46

ChemAxon Workshop Presentation

Title: Building on JChemBase

Author: Szilard Dorant

Institution: ChemAxon

Abstract:The workshop will cover various aspects of JChem Base integration, including:

- Explaining the structure of JChem Base applications

- Memory considerations

- Performance tips

- Displaying hits

- Filtering duplicate structures

- API examples

- Upgrade issues

ChemAxon 0815c054e1

13-06-2006 16:43:53

ChemAxon Workshop Presentation

Title: Fine tuning JChem Cartridge

Author: Peter Kovacs, Szilard Dorant

Institution: ChemAxon

Abstract:Granting user privileges

- one example with JChem tables, one with regular structure tables


- Rearranging queries to use filter queries and/or composite queries

- using multiple query structures with a single search (with OR-d results)

- impact of cache update (DELETE with JChem tables versus regular tables)

- delay index update with regular structure tables

Search types (exact, exact-fragment)

- clarifying difference (is it obvious for the typical user?)

Time travel with JChem Cartridge (as a result of statement-level read consistency)

- a simple example

The code for the examples is available at http://www.chemaxon.com/shared/pkovacs/ugm2006_workshop/

ChemAxon 0815c054e1

13-06-2006 16:45:53

ChemAxon Presentation

Title: ChemAxon future, Q&A

Author: Szabolcs Csepregi

Institution: ChemAxon


General directions of ChemAxon

New products and solutions

Evaluation of wish-list sheets

Questions & Answers

ChemAxon 0815c054e1

13-06-2006 16:47:09

ChemAxon Presentation

Title: Markush Search and enumeration - new development

Author: Szabolcs Csepregi

Institution: ChemAxon


What is Markush?

Targeted Markush features at current stage

Markush drawing in Marvin

Into the database and searching

Enumeration – counts, types

Markush aromatization – Ambiguous aromaticity

Project timelines

Future plans