Posted: Thu Oct 01, 2009 3:38 pmPost subject: Tautomers: A Rant
Title: Tautomers: A Rant
Presenter: Yvonne Martin
Institution: Martin Consulting
Abstract: Approximately 25% of all drug-like molecules exist as more than one tautomeric form. This affects all aspects of computer-aided molecular design. One challenge is that frequently biomacromolecules bind a rare tautomer, which may not be enumerated by a tautomer generation program. A second challenge is to devise a database scheme that will enable one to store observations on both the structures and the tautomeric ratios of a compound as observed or calculated in different environments. A third challenge is to decide how or whether to include tautomers as a result of a substructure or similarity search--should only 'predominant' tautomers be searched and reported, or 'all'?
Posted: Thu Oct 01, 2009 3:40 pmPost subject: What's new and what's coming in Instant JChem
Title: What's new and what's coming in Instant JChem
Presenter: Tim Dudgeon
Abstract: Instant JChem has undergone significant change over the last year. Various new features will be demonstrated; a simple way to do reaction based enumeration within an Instant JChem database, support for new data types such as images, html, documents etc, URL fields allowing you to link in and link out to information on your network of the internet, the ability to handle chemical terms functions that generate structures, improved printing, improved schema editor and ability to connect to existing databases, table and column level access control, added ability to copy forms
Posted: Thu Oct 01, 2009 3:58 pmPost subject: Cost effective cheminformatics for small chemistry teams int
Title: Cost effective cheminformatics for small chemistry teams integrated within larger discovery groups
Presenter: John McNeil
Institution: John McNeil & Co
Abstract: Not all biotechnology companies are focused on small molecule drug discovery, nor do they need to manage millions of compounds. However, these companies do synthesize novel compounds and must track related data. For example, Ambrx, Inc.'s discovery platform is based on a fundamental advance in protein biosynthesis that enables the company to genetically engineer proteins with new amino acid building blocks beyond the common twenty. Ambrx has a small, active, chemistry group that wishes to register compounds, assign identifiers, track batches, and associate analytical data. The cost of most chemistry registration systems force chemistry groups like these to do without. Ambrx uses our open source LabSynch software to track, analyze, report and share its protein-based drug discovery samples and data. We will describe how we integrated Instant JChem Enterprise with LabSynch to enable Ambrx to associate chemistry structure, batch and analytical data with their other discovery data.
Posted: Thu Oct 01, 2009 4:02 pmPost subject: Virtual synthesis and metabolism - new developments
Title: Virtual synthesis and metabolism - new developments
Presenter: György Pirok
Abstract: ChemAxon's Reactor technology has recently been integrated in the Instant JChem platform providing an easy to use interface for combichem library generation in databases. A new application called Metabolizer predicting major metabolites of xenobiotic compounds using biotransformation libraries will be introduced also.
Posted: Thu Oct 01, 2009 4:13 pmPost subject: Experiences with Reactor in Pipeline Pilot
Title: Experiences with Reactor in Pipeline Pilot
Presenter: Isabella Haight
Institution: Abbott Laboratories
Abstract: Virtual libraries are potentially a source of novel compounds which could be used in virtual screening, lead optimization and lead hopping. In order for a virtual compound library to be of use to a scientist, it should be synthetically accessible, with a well defined reaction scheme that uses readily available starting materials. ChemAxon’s Reactor supports 'smart' reactions for generating chemically feasible products. Integration of Reactor as a Pipeline Pilot component allows for intelligent enumeration of reactions with the ability to further process the output all in one platform. The utilization of some recent improvements to the Reactor component for Pipeline Pilot will be highlighted.
Posted: Fri Oct 02, 2009 10:43 amPost subject: Cheminformatics approaches for metabolomics research
Title: Cheminformatics approaches for metabolomics research
Presenter: Tobias Kind
Institution: UC Davis Genome Center - Metabolomics
Abstract: Metabolomics is part of the modern life sciences tree including genomics, transcriptomics and proteomics. One of the major goals in metabolomics is to identify small molecules including lipids, organic acids, sugars and amino acid and to obtain spatial and temporal snapshots of metabolite concentrations from complex biological matrices. The results are used to obtain greater insight into plant and animal metabolism and to understand complex cellular processes. Cheminformatics approaches play a crucial role in metabolomics because properties of organic molecules can be modeled in-silico and are matched against experimentally obtained result from analytical techniques including liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS). The accuracy of such predictions including octanol water partition coefficients (logP), acid dissociation constants (pKa) and boiling points (bp) are important to reduce the search space from millions of possible structural isomers down to a low number of potential candidate structures. Besides that, cheminformatics software tools must be able to handle millions of structures and a multitude of structure formats and should provide simple-to-use graphical front ends for novice users and versatile command line parameters for experts. We used Marvin GUI components including ChemAxon MView, Standardizer and Reactor as well as the JAVA API components in a metabolomics environment to generate molecular structures and curate mass spectral databases. The use of such databases allows the measurement of more than 150 metabolites in a single sample, requiring only few micrograms of biological material. Using our high-throughput analytical techniques we are able to profile several thousand samples per year. In addition to that, we show how the Instant-JChem program with its integrated overlap search and Marvin tools can be used as a general purpose tool for structure handling. We show how physico-chemical property calculations obtained from Marvin are used to support the structure elucidation process in metabolomics.
Posted: Fri Oct 02, 2009 10:44 amPost subject: Marvin new features and future plans
Title: Marvin new features and future plans
Presenter: Akos Papp
Abstract: Since the last US UGM several new features have been developed in Marvin, and many more are under development. This presentation will summarize these features, and most of them will be demonstrated online. Some features to be released in version 5.3 will already be shown in work, like the Sprout drawing and the enhanced bracket drawing functions, as well as the Chemical Terms editor placed inside the MarvinSketch user interface. The development of the .Net version of MarvinSketch and MarvinView is also in an advanced phase, which will be presented through the demo of their standalone versions.
Posted: Fri Oct 02, 2009 12:26 pmPost subject: SPrime: Computational Chemistry Application and Framework fo
Title: SPrime: Computational Chemistry Application and Framework for Drug Discovery
Presenter: Hongzhou Zhang
Institution: Eli Lilly and Co.
Abstract: We have designed SPrime (System for Predictive In-silico Method) - a new computational chemistry application and framework for drug discovery. It enables scientists to design library of molecules, generate and evaluate hypothesis, predict properties and analyze structure and activity relationship. One essential element of the system is the integration of Java-based Chemaxon Marvin UI into the .net based application.
Posted: Fri Oct 02, 2009 12:27 pmPost subject: What's new in JChem back-end
Title: What's new in JChem back-end
Presenter: Szabolcs Csepregi
Abstract: JChem Base is a chemical database management toolkit to handle molecules, chemical reactions and Markush structures and associated data stored in relational databases. JChem Cartridge provides similar functionality highly integrated into Oracle as well as an SQL interface to other ChemAxon products. This presentation will briefly overview the two above systems and the latest and near future developments will 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, R-group decomposition, etc
Posted: Fri Oct 02, 2009 12:33 pmPost subject: An Educational Tool for Learning Substructure Search
Title: An Educational Tool for Learning Substructure Search
Presenter: Yingyao Zhou
Institution: Genomics Inst. of the Novartis Research Foundation
Abstract: Substructure searches provide expected results, only if users are familiar with the structure query language. Understandably teach and practice are the best ways to improve such language skills, therefore, we developed a corresponding educational tool at GNF. Given a query structure, the tool automatically supplies example targets. Then through interactively modifying the query structure and subsequently highlighting matched structure fragments, users learn to improve the accuracy of the search. The tool can also incorporate predesigned examples, as well as being used for sanity checking before a real database search.
Posted: Fri Oct 02, 2009 12:41 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 interfaces will be discussed, such as the pure .NET interface, Oracle Cartridge, and workflow platform integrations.
Posted: Fri Oct 02, 2009 12:42 pmPost subject: ChemAxon for SharePoint
Title: ChemAxon for SharePoint
Presenter: Tamas Pelcz
Abstract: Microsoft SharePoint Server is becoming the standard portal platform at many major pharmaceutical companies. It lets scientists to easily share and manage research and discovery data. ChemAxon's SharePoint extensions enable chemistry inside SharePoint not only on the enterprise, but also at the individual level. Manage and filter for structures inside lists, wikis, blogs and discussion boards. Custom calculation column type allows to display structural property predictions in lists. Import from, and export to various chemical file formats. There are plans for integration with desktop apllications, allowing enterprise wide structure search, charting, and integrationg various other tools in SharePoint.
Posted: Fri Oct 02, 2009 12:42 pmPost subject: ASAP - Emphasizing Multidimensional Drug Discovery
Title: ASAP - Emphasizing Multidimensional Drug Discovery
Presenter: Pat Walters
Institution: Vertex Pharmaceuticals
Abstract: One of the biggest challenges facing drug discovery teams is extracting information from the large volume of data generated in the course of a lead optimization effort, and using this information to make decisions. A typical lead optimization project can track between 15 and 30 assays (enzyme, cell, properties, PK, etc), and identifying trends in this data can be difficult. In an effort to address this problem and help scientists to make better decisions, we have developed a new software platform called ASAP. ASAP provides an intuitive overview of the data that also allows scientists to easily 'drill down' and examine the details of particular experiments. A combination of 'filters' and heat maps allows teams to focus on aspects of the data while remaining aware of the 'big picture'.
Posted: Fri Oct 02, 2009 12:43 pmPost subject: ChemAxon in 3D
Title: ChemAxon in 3D
Presenter: Miklos Vargyas
Abstract: Conventional ChemAxon technologies focus on bare topological features of molecules and ChemAxon have been recognised as a 2-dimensional company that provides cheminformatics tools. Yet, ChemAxon have been active in the 3D world of molecular modelling 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. The 3D world of ChemAxon will be presented (in 3D).
Posted: Fri Oct 02, 2009 12:56 pmPost subject: Macromolecular Structure Notation, Editing and Registration
Title: Macromolecular Structure Notation, Editing and Registration
Presenter: Tianhong Zhang
Abstract: While many software systems exist for small molecule structure representation, drawing and registration and are widely used by biotech/pharmaceutical companies in small molecule drug discovery, there is no system available designed specifically for large molecules. This talk begins with a review of the challenges in large molecule structure representation and the shortcomings in using small molecule systems for large molecules. A notation language to represent large molecule structure will be presented, and examples will be provided on how to use it for modified oligonucleotides and peptides. A Graphic User Interface (GUI) tool will then be presented to demonstrate how to construct a complex large molecule structure, such as siRNA with chemical modifications. Finally, the talk will discuss a large molecule registration system, with focus on structure uniqueness checking, validation and verification.
Posted: Fri Oct 02, 2009 12:56 pmPost subject: IUPAC Naming and chemicalize.org
Title: IUPAC Naming and chemicalize.org
Presenter: Daniel Bonniot de Ruisselet
Abstract: A very large number of webpages, 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: Fri Oct 02, 2009 12:57 pmPost subject: Applying ChemAxon name-structure to chemical patent data
Title: Applying ChemAxon name-structure to chemical patent data
Presenter: Nicholas Goncharoff
Abstract: We examine the results of using ChemAxon's new name-to-structure conversion tool on the SureChem database of full-text patent documents. We further compare ChemAxon's performance with that of other name-to-structure tools currently used in the SureChem data generation pipeline.
Posted: Fri Oct 02, 2009 1:26 pmPost subject: A JChem Webservices Application using Adobe Flex
Title: A JChem Webservices Application using Adobe Flex
Presenter: Julio Carneiro
Institution: SkunkWerks Software
Abstract: SkunkWerks used JChem to provide substructure and similarity searches across an existing Screening Library System. The solution was integrated with the existing RIA applications and SkunkWerks proprietary back end. SkunkWerks opted for JChem's Web Services as the means to communicate with JChem Base. Using JChem's Web Services SkunkWerks was able to seamlessly integrate substructure/similarity searches into the application. This session will present the solution that was developed using JChem and Flex (Adobe Flex) for a RIA implementation.
Posted: Fri Oct 02, 2009 1:26 pmPost subject: Command line tools of ChemAxon: tips and tricks
Title: Command line tools of ChemAxon: tips and tricks
Presenter: Gyorgy 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 utilites 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: Fri Oct 02, 2009 1:35 pmPost subject: Building a RESTful DrugBank Structure Resource Using Ruby on
Title: Building a RESTful DrugBank Structure Resource Using Ruby on Rails and JChem Base
Presenter: Craig Knox
Institution: University of Alberta
Abstract: To facilitate the creation of a central structure hub for databases such as DrugBank and the Human Metabolome Database at the University of Alberta, we have integrated JChem Base with Ruby on Rails, a robust web-application framework. By using JRuby to bridge the Java and Ruby world, we have built a scalable solution for storing, retrieving, and searching structures. This presentation will discuss the implementation details and advantages of building a simple, standard, and web-accessible structure hub.
Posted: Fri Oct 02, 2009 1:37 pmPost subject: JChem for Excel
Title: JChem for Excel
Presenter: Tamas Pelcz
Abstract: JChem for Excel allows scientists to use ChemAxon toolkit in Microsoft's familiar spreadsheet application. Easily add, edit and delete structures, with full 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. The API allows for integration with external applications, or VBA based customizations. With the help of fustom chemical excel functions, calculate molecular properties, display calculated properties as images such as atomic charges, pKa , HBDA and so on. The newly introduced, and unique structure resulting functions opens up a new dimension of operations in Excel. It is possible to display tautomeric forms, stereoisomers, structural frameworks, convert to standard representational forms, and run virtual synthesis.
Posted: Fri Oct 02, 2009 1:42 pmPost subject: The New JKlustor Suite
Title: The New JKlustor Suite
Presenter: Miklos Vargyas
Abstract: JKlustor, ChemAxon's first package providing capabilities beyond core cheminformatics has been intensively developed in the past few years. Diverse problems ranging form the crude and fast clustering of million structure company database to the meticulous hierarchical clustering of VHTS hit sets can be tackled by the most appropriate method. Some of these will be presented on worked examples.
Posted: Fri Oct 02, 2009 1:45 pmPost subject: 'Natural' Clustering: An approximate MCES algorithm used on
Title: 'Natural' Clustering: An approximate MCES algorithm used on WOMBAT
Presenter: Oleg Ursu
Institution: University of New Mexico
Abstract: We describe a clustering procedure for chemical compounds, which can rapidly be deployed on large compound libraries. The procedure creates initial cluster seeds starting from fingerprints and the Taylor-Butina algorithm (as implemented by MESA Analystics). After fast initial seeding the clusters are refined and rearranged using an approximate solution of the MCES (Maximum Common Edge Substructure) algorithm. The chemical patterns identified during fingerprint clustering are subject to filtering rules to ensure homogeneity of the clusters. The approximate MCES algorithm (RASCAL implementation) is then applied to identify shared chemotypes in an iterative manner until all chemical structures in the library are assigned to the appropriate cluster. We tested this procedure on the WOMBAT database, which presented a 'natural' clustering solution, i.e., the series reported within WOMBAT (from SUNSET Molecular) that were used to identify common patterns and evaluate algorithmic performance.
Posted: Fri Oct 02, 2009 1:48 pmPost subject: Markush structures at ChemAxon
Title: Markush structures at ChemAxon
Presenter: Szabolcs Csepregi
Abstract: Markush structure handling at ChemAxon range of products will be presented, including drawing, visualization and generation of Markush structures, Markush enumeration techniques and searching. It will be shown how libraries more complex than 1030 library size are handled, with the generic description including R-groups, atom and bond lists, link nodes, repeating groups, position variation and homology groups. A focus will be given to latest developments: Homology groups: searching and sampling enumeration, Repeating groups and position variation, Ways of Markush structure creation: reagent clipping, R-group decomposition, VMN import to access patent Markush structure databases.
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