Posted: Wed Jun 10, 2009 11:07 amPost subject: Compound databases and project management with Instant JChem
Title: Compound databases and project management with Instant JChem and JChem
Presenter: Gert Thijs
Abstract: Silicos is a chemoinformatics-based biotechnology startup focusing on early-phase drug discovery. We have initiated several in-house drug discovery projects and also provides services in the field of virtual screening and de novo design using its proprietary technologies, SpectrophoresTM and CosmosTM. In this talk we would like to give some insight in the use of InstantJChem and JChem in our day-to-day research and project work. To support our in-house development, we needed to set up a small, but rapidly expanding, compound registration system in which we could store both purchased and synthesized compounds. The first goal is to be able to keep track of where compounds came from and how much and in which state they are stored. But more importantly the system should also be easily extensible with biological data as the compounds are tested in the lab in the different projects. To facilitate the maintenance of the database we developed several small programs to upload new compounds and keep the data consistent. In case of our virtual screening activities we created a large database of more than 6 million commercially available compounds, called Simosa. These compounds have all been processed in a standardized way to make them ready for deployment with our virtual screening tools on our cluster. In this setup we need to have easy access to the vendor data of a specific compound and to find structurally similar compounds. The main challenge here is to keep the database up to date with new vendor catalogs and keep track of the older and unavailable compounds so that we can easily order compounds. Since the database is very large it is important to provide an interface to the modelers where they can create subsets of compounds which can be handled more conveniently on their local laptop with InstantJChem. To make these databases accessible we combined both the power of InstantJChem and JChem to create small command line programs that can be easily called from our scripts to query the databases.
Posted: Wed Jun 10, 2009 11:43 amPost subject: Marvin features and news
Title: Marvin features and news
Presenter: Ákos Papp
Abstract: The Marvin package consists of applications for drawing and visualization of chemical structures and reactions. This presentation will focus on the main features of MarvinSketch and MarvinView, giving special attention to the latest improvements, like transparent images, enhanced bracket drawing, or accelerated viewing of huge structure files. Details on the ongoing developments, like the .Net and the lite versions, as well as the future plans will also be disclosed.
Posted: Wed Jun 10, 2009 12:02 pmPost subject: Title: What's new in JChem back-end and Markush storage, sea
Title: What's new in JChem back-end and Markush storage, search and enumeration.
Presenter: Szabolcs Csepregi
Abstract: JChem Base is a chemical database management toolkit to handle molecules, chemical reactions and Markush structures and associated data (user-defined or predicted), stored in relational databases. JChem Cartridge provides similar functionality highly integrated into Oracle as well as an Oracle interface to other ChemAxon products.
This presentation will overview the two above systems, with special attention to Markush structure storage, searching and enumeration. Latest and near future developments will also be introduced including: position variation queries and repeating groups, attached data and polymer representation, undefined R-atom searching, homology groups (alkyl, aryl, etc.), performance improvements, example AJAX client and Web Services interface, new metrics and other improvements for similarity search, installation improvements, registration system API.
Posted: Wed Jun 10, 2009 12:42 pmPost subject: Developing with ChemAxon at Evotec - some case studies
Title: Developing with ChemAxon at Evotec - some case studies
Presenter: Catherine Reisser
Abstract: At Evotec we have been developing software using ChemAxon tools for more than five years. This talk will provide an insight into some of the applications that we have been building over the past year - including a new Web 2.0 Compound Ordering system connected to our own compound supplier database and the Symyx ACD and our ERP system, enhancements to our registration system that we introduced last year including handling tautomers, overlap searching and export preferences using the JChem cartridge.
Posted: Wed Jun 10, 2009 12:48 pmPost subject: Interfacing the JChem Suite outside of Java (Web Services, .
Title: Interfacing the JChem Suite outside of Java (Web Services, .NET, and SQL)
Presenter: Jonathan Lee
Abstract: Discover the alternative interfaces to the JChem Suite of tools without direct Java programming. This will be an introductory look at the Web Services architecture and the services available. Other .NET and SQL interfaces will be discussed, such as JNBridge and Cartridge.
Posted: Wed Jun 10, 2009 12:50 pmPost subject: Complementarity between Public and Commercial Databases of B
Title: Complementarity between Public and Commercial Databases of Bioactive Compounds
Presenter: Sorel Muresan
Abstract: Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding.
This work updates a previous comparative study [Southan, C.; Varkonyi, P.; Muresan, S. Current Topics in Medicinal Chemistry 2007, 7, 1502] of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets.
Posted: Wed Jun 10, 2009 12:51 pmPost subject: Command line tools of ChemAxon: tips and tricks
Title: Command line tools of ChemAxon: tips and tricks
Presenter: György Pirok
Abstract: ChemAxon offers a comprehensive API for programmers accessing all classes and functionalities of the JChem toolkit. Database developers often use SQL statements via the ChemAxon cartidge for the same purpose and chemists can enjoy the graphical applications like Instant JChem. It is less known, however, that ChemAxon provides a rich set of command line utilities that are sometimes more simple and powerful than the above mentioned interfaces. Some command line utilities will be demonstrated presenting how you can convert molecules, how to store calculated properties and complex descriptors in SDFile fields, and how to search quickly in files or databases....
Posted: Wed Jun 10, 2009 12:54 pmPost subject: Cheminformatics in the Cloud
Title: Cheminformatics in the Cloud
Presenter: Michael Dippolito
Abstract: In response to increasing demand for software as a service and hosted cheminformatics solutions, DeltaSoft and ChemAxon have teamed up to provide a suite of fully hosted applications, including compound registration, inventory, bioassay, and structure activity searching and reporting. The hosted solutions free IT groups from the installation, ongoing maintenance and upgrades of hardware and software infrastructure. Users can access applications and data anywhere from a web browser. The details of this approach and various implementation options will be discussed in this presentation.
Posted: Wed Jun 10, 2009 1:04 pmPost subject: The Pistoia Alliance: An Emerging Cross-pharma Collaboration
Title: The Pistoia Alliance: An Emerging Cross-pharma Collaboration
Presenter: Richard Bolton
Abstract: An Open Source initiative known as the Pistoia Partnership has been established to streamline non-competitive elements of the pharmaceutical drug discovery workflow by the specification of common business terms, relationships and processes. Initial focus has been on chemistry, biological screening and sample logistics.
Every pharma company & software vendor is challenged by the technical interconversion, collation and interpretation of drug/agrochemical discovery data, and as such, there is a vast amount of duplication, conversion and testing that could be reduced if a common foundation of data standards, ontologies and web-services could be established within a nonproprietary and non-competitive framework. Such would allow interoperability between a traditionally diverse set of technologies to benefit the healthcare sector.
Through global collaboration, this pragmatic community will derive, instantiate and make available web-services for consumption by Academic institutions, Vendors and Companies under an Open Source framework.
We will describe current progress, learnings and how companies, academics and others can participate in this approach.
Posted: Wed Jun 10, 2009 1:11 pmPost subject: ChemAxon in 3D
Title: ChemAxon in 3D
Presenters: Miklós Vargyas
Abstract: Conventional ChemAxon technologies focus on bare topological features of molecules and ChemAxon has been recognised as a 2-dimensional company that provides cheminformatics tools. Yet, ChemAxon has been active in the 3D world of molecular modeling for some time. The first break with the 2D tradition was marked by the release of the 3D structure generator that later evolved into a 3D multi-conformation plugin. The next milestone was the release of MarvinSpace, our 3D molecular structure and surface visualiser tool.
The most recent developments include 3D flexible alignment, 3D volume overlay and 3D virtual screening by 3D molecular descriptors.
Posted: Wed Jun 10, 2009 1:14 pmPost subject: Universal chemistry searching in text documents
Title: Universal chemistry searching in text documents
Presenter: Lutz Weber
Abstract: OCMiner is OntoChem’s chemistry aware semantic search engine. Based on UIMA, OCMiner allows to annotate and subsequently search various information sources with concepts from chemistry, biology and related disciplines. Chemical structure searching, including sub-structure and similarity searches using ChemAxon functionalities as well as ontology based concepts are added to a Lucene based free text searching.
Posted: Wed Jun 10, 2009 1:15 pmPost subject: IUPAC Naming and chemicalize.org
Title: IUPAC Naming and chemicalize.org
Presenter: Daniel Bonniot de Ruisselet
Abstract: A very large number of web pages, patents, text, office and PDF documents contain chemical names, which constitute valuable information. However, since the names are mixed in the text, without specific markup or associated chemical representation, it can be very difficult to identify and use this information. We present a set of technologies that solve this problem by detecting chemical names inside free text, converting the names to chemical structures, and annotating the original document with this added information. These technologies are combined to power the chemicalize.org website, a free public service that acts as a proxy rendering any publicly accessible website with added chemical annotations. With these annotations it then becomes possible to perform rich chemical searches (for instance sub/super-structure searches) on the set of indexed documents. We present the underlying name-to-structure and structure-to-name tools, and their improvements over the past year.
Posted: Wed Jun 10, 2009 1:17 pmPost subject: Chemical Entity extraction using the chemicalize.org -techno
Title: Chemical Entity extraction using the chemicalize.org -technology
Presenter: Josef Scheiber
Institution: Novartis Pharma
Abstract: We will present an early implementation of the chemicalize.org-technology (chemical entity recognition + name2struct) into a tool that is used for text mining purposes.
This will enable users to paste any text from any source and possible entities are recognized (other technologies + dictionaries used for biology etc.) to enable further analyses. Possible use cases are also shown.
Posted: Thu Jun 11, 2009 7:59 amPost subject: Chemical data management in the real world - buy or develop,
Title: Chemical data management in the real world - buy or develop, data sharing and helping the scientists to work more effectively
Presenter: Ian Berry
Abstract: In the current climate, cost and effectiveness is vital for survival. At Evotec we are seeking to improve our ability to manage chemical data, to share that data more effectively with our clients and to allow our scientists to work more efficiently through automation of data management. The decision to buy software such as an ELN, or products such as Instant JChem help to provide the scientists with the basic tools to do their job. By enhancing these through integration, extension and enhancement by our in-house software team we aim to allow them to do their job in a more efficient and (cost-)effective way. This talk will discuss our decision process for choosing an ELN (to work with ChemAxon tools), our plans for Instant JChem and data sharing with clients.
Posted: Thu Jun 11, 2009 8:01 amPost subject: Instant JChem - current status and what's coming soon
Title: Instant JChem - current status and what's coming soon
Presenter: Tim Dudgeon
Abstract: Instant JChem is ChemAxon's desktop cheminformatics solution for chemists and biologists. Current features includes powerful import/export functionality supporting a wide range of data formats, reporting using SAR tables and a form builder, sophisticated structure and non-structure search capabilities and the ability to design and manage local and remote chemical databases.
This talk will describe how these basic features are now being extended to meet the needs of customers who are wanting to use IJC as a reporting tool and to manage more complex types of data.
Posted: Thu Jun 11, 2009 8:02 amPost subject: Training pKa and logP prediction
Title: Training pKa and logP prediction
Presenter: József Szegezdi
Abstract: pKa and logP prediction methods are based only on a limited number of molecule types in the training set. The accuracy of these models is not always satisfactory. Practically, in most cases only those types of structures will be predicted correctly which were present in the training set. We decided to develop a training method for the pKa and the logP calculations to allow users to build models relevant for their structures.
The identification of acidic and basic ionization centers is defined in our default pKa prediction module. 120 predefined atom types are implemented in the logP prediction model. The learning algorithm is based on a linear regression method called as Single Value Decomposition (SVD). The training set, a collection of experimental pKa or logP values, should be provided by the user. The collected data should be imported as an SDF or MRV file, which can be compiled for example using Instant JChem.
Posted: Thu Jun 11, 2009 8:09 amPost subject: A knowledge-based approach for reaction generation
Title: A knowledge-based approach for reaction generation: development, validation and applications
Presenter: Dimitar Hristozov
Institution: Eli Lilly
Abstract: We present a new method for knowledge-based driven reaction generation. The structural changes at the reaction centre are described using reaction vectors1. The reaction vectors are derived automatically from a database of known organic reactions even when no atom-atom mapping information is available. A structure generation algorithm which allows the application of reaction vectors to previously unseen starting materials has been developed. The method reproduces known reactions with a success rate higher than 90%. Its applications in different medicinal chemistry related scenarios and its implementation using Knime2 and ChemAxon’s libraries are discussed.
1 Patel, H., Bodkin, M.J., Chen, B., Gillet, V.J.A Knowledge-Based Approach to De Novo Design Using Reaction Vectors, J. Chem. Inf. Model., 2009, accepted for publication 2 KoNstanz Information MinEr (KNIME), http://www.knime.org/
Posted: Thu Jun 11, 2009 8:17 amPost subject: Prediction of xenobiotic metabolism and major metabolites
Title: Prediction of xenobiotic metabolism and major metabolites
Presenter: György Pirok
Abstract: Compounds foreign to an organism's normal biochemistry are metabolized by enzymatically catalysed biotransformations. That process plays an important role in the detoxification of poisonous molecules, but sometimes intermediers themselves can be responsible for toxic effects. The prediction of metabolic fate is a complex problem, yet it can help in the evaluation of experimental results, in the estimation of metabolic stability, as well as the early identification of potential toxicity risks. A new software application called Metabolizer has been developed to enumerate all metabolites and to predict the major ones of the given drugs or other xenobiotics. The results can be influenced by the replacement or the modification of the biotransformation libraries used. The prediction model and the calculations of the key indicators will be explained, and the first release version of the Metabolizer application will be introduced.
Posted: Thu Jun 11, 2009 8:20 amPost subject: Applying ChemAxon name-to-structure technology to SureChem p
Title: New kid on the block: Applying ChemAxon name-to-structure technology to SureChem patent chemistry database
Presenter: Nicholas Goncharoff
Abstract: SureChem's database of more than 9 million chemical structures is generated by extracting chemical names from full text patents and converting them to chemical structures using a suite of name-to-structure conversion tools. SureChem has performed an evaluation of ChemAxon's newly developed name to structure toolkit, comparing the results to those obtained by the other tools in SureChem's current production pipeline. Results of that comparison and suggestions for future developments will be discussed.
Posted: Thu Jun 11, 2009 8:23 amPost subject: JChem for Excel
Title: JChem for Excel
Presenter: Tamás Pelcz
Abstract: JChem for Excel allows scientists to use ChemAxon toolkit in Microsoft's familiar spreadsheet application. Easily add, edit (on double click) and delete structures, with undo support. Structures move and size with cells, so operations such as copy(cut) - paste, sorting and filtering run smoothly. Import structures/data from, and export to popular chemical file formats, and import from various databases. Calculate molecular properties with the help of custom chemical excel functions.
Posted: Thu Jun 11, 2009 8:25 amPost subject: Chemistry searching in the cloud based ELN, iLabber
Title: Chemistry searching in the cloud based ELN, iLabber
Presenter: Andy Mott
Institution: Contur Software
Abstract: An electronic lab notebook (ELN) contains a lot of unstructured data including chemical structures and reactions. A cloud based ELN does not allow for customization or integration with other systems. Chemical searching must be enabled in a way that allows users to find their information without restricting the way they enter data. The way iLabber uses the Jchem to meet this will be discussed.
Posted: Thu Jun 11, 2009 8:27 amPost subject: The New JKlustor Suite
Title: The New JKlustor Suite
Presenter: Miklós Vargyas
Abstract: JKlustor, ChemAxon's first package providing capabilities beyond the core cheminformatics, offers versatile clustering techniques. Diverse problems ranging form crude clustering of million structure company database to fine scale hierarchical clustering of VHTS hit sets can be tackled by the most appropriate method. Some of these will be presented on worked examples.
Title: Metabolic Pathway Builder: Connecting, completing and exploring biochemical and genomic data
Presenter: Sophie Huet, Pierre-Emmanuel Ciron
The knowledge on the connections between the genome, the proteome and the metabolome of an organism is a key to a global understanding of the dynamics of its cells: the metabolic reactions, which produce energy and transform small molecules necessary for the cell to operate, are catalyzed by enzymes, which, as proteins, are synthesized according to the information coded in the genes. Metabolic Pathway Builder (MPB) has been designed to help biologists annotating genomic sequences, i.e. identifying the coding sequences and characterizing the proteins they code for. Some of these proteins are enzymes and MPB provides methods for predicting the metabolic reactions they catalyze. MPB makes use of the Chemaxon library for managing and displaying chemical compounds and metabolic reactions. In MPB, the links between genes, proteins and reactions are indeed modeled in a large entity - relationship network that can be browsed and queried. For instance, in the context of spectrometry analysis, a powerful query relies on the structural search facility of JChem Base. It retrieves all the metabolites which share a chemical substructure; the metabolic reactions and pathways which involve these metabolites can be further identified and displayed by MPB, together with the genes the products of which catalyze the reactions of the pathways. Integrating other functions provided by the Chemaxon library will allow Metabolic Pathway Builder to extend its capacities further in the direction of chemoinformatics. Genostar is particularly interested in increasing the connections between its software modules and external biochemical and chemical databases, and the 3D-visualization capabilities.
Posted: Fri Jun 12, 2009 10:45 amPost subject: Developing a JChem based web application for searching...
Title: Developing a JChem based web application for searching compounds in vendor databases
Presenter: Márk Sándor, Dániel Kozma, László Molnár
Institution: Richter Gideon
Using JChem Cartridge and JChem Base functionalities a web application was developed for searching in vendor databases collected by the molecular modelling group of Gedeon Richter plc. The initial state of lead discovery usually begins with virtual screening, our web application and the underlaying database serves as starting point for our virtual screening studies.
Posted: Fri Jun 12, 2009 10:46 amPost subject: Evaluating small molecular libraries using molecular do...
Title: Evaluating small molecular libraries using molecular docking and binding profile analysis.
Presenter: Annamária F. Ángyán1,2, Gábor Iván1,2 and Vince Grolmusz1,2
Institutions:1 Protein Information Technology Group, Eötvös Loránd University, Budapest, Hungary, 2 URATIM Ltd., Nyíregyháza, Hungary
Abstract: In drug design and discovery, biologically active small molecules are identified, then their derivatives are screened for better biological or pharmacological properties. In this optimization phase it is frequently helpful to generate large sets of small molecules by exchanging some parts of the basic, biologically active molecule to numerous molecular fragments. This way thousands of molecular derivatives called molecular libraries can be automatically generated. In most of the cases biological activity of small molecules depends on binding to large protein molecules in the cell. In this work we present some mathematical tools capable of evaluating the binding of molecular libraries to protein molecules, yielding tools for drug discovery and design.
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