Over 150 people in total participated in the workshops. Thank you for your participation! The presentation DiscoveryGate (Alexander Kos), and Reaction Searching in DiscoveryGate (Guenter Grethe) are available as downloads: DiscoveryGate (ca. 5 MB) Searching in DiscoveryGate (ca. 4 Mb) In the case that you want to use the slides in your own presentations, please reference them properly, thank you. We also have some additional information material for the Patent Chemistry Database: PCD Brochure (ca. 1MB) Molcon Article (Ca. 1.4 MB) Chemoinformatics Workshops ChemInfo 2006 We give two workshops in the Czech Republic and few more in Poland. If you live close to the border to Poland you might have a look at the Internet, and choose a place in Poland. Please make sure you register for the correct event. After May 5th, you will not get any more a confirmation of your registration. The workshop in Prague is more extensive. People from Elsevier Science will present Scopus and give an overview of other Elsevier products. My talk about DiscoveryGate is an on-line demonstration of the system. Dr. Grethes talk about reaction searching is purely educational, and we hope many students take the opportunity to learn that a lot of time of the synthetic chemist is spend in front of the computer. The other presentations of chemoinformatics methods are also educational, and teach what kind of methods are required in modern industrial pharmaceutical research. A perfectly formatted version of this document is at http://www.akosgmbh.de/cheminfo2006.
Brno Agenda for Wednesday May 10, 2006
Location: Masaryk University
Time: 10:00
Contact: Dr. Ctibor Mazal, Department of Organic Chemistry, Masaryk University, Kotlarska 2, +420-5-41129303, mazal@chemi.muni.cz 10:00 DiscoveryGate (Alexander Kos)
11:00 Coffee Break
11:15 Reaction Searching in DiscoveryGate (presenter Dr. Guenter Grethe)
12:00 12:30 Break
12:30 Discussion and demonstration of other programs, i.e.(Alexander Kos und Guenter Grethe)
Prague Agenda for Monday May 22nd
Location: Institut of Chemical Technology, Technicka 5, training room of the library
Time: 9:30
Contact Person: Dr. Jaroslav Silhanek. Institut of Chemical Technology, Technicka 5.+420 (220) 444 183, jaroslav.silhanek@vscht.cz 09:30 10:15 DiscoveryGate (Alexander Kos)
10:15 11:05 Reaction Searching in DiscoveryGate (Guenter Grethe)
11:05 11:20 Break
11:20 12:15 MDL Patent Chemistry Database (Eva Seip)
12:15 13:15 Lunch
13:15 14:00 Scopus and its integration with DiscoveryGate (Sandra Grijzenhout)
14:00 14:45 Access to electronic journals (Piotr Golkiewicz or Sandra Grijzenhout)
14:45 15:00 Break
15:00 15:45 PASS - a program for in silico screening
15:45 16:15 Personal Chemist Client
16:15 16:30 Quantum Molecular Modelling Package
16:30 17:00 MDL Notebook and Isentris, a platform and architecture to access personal, and on-line information We are available for discussion after 17:00, and participants can use the computers in the training room.
Overview: Chemo and bioinformatics tools are here to generate, and to handle new dimensions of data. Our task is to introduce you to these tools, give you an understanding of their possibilities and offer solutions that enable the researcher to find answers, instead of spending undue time in getting proficient in the use of a computer program. AKos GmbH is the provider of the largest collection of databases, and software for chemical research & development in your area. We would like to give an overview of our product portfolio in a workshop with presentations and life demonstrations. The workshop will be organized with the help of Elsevier MDL and Elsevier Science. Registration:Please register by sending an email with full name and address to akos@akosgmbh.de. Dont forget to indicate for which event you will register. The participation is free of charge. We will serve beverages. Please register immediately and you make it easier for us to organize the event. Background Information: DiscoveryGate: All Elsevier MDL databases are accessed under one user interface via the Internet portal DiscoveryGate (www.discoverygate.com). - DiscoveryGate is the comprehensive gateway to chemical information. It covers basically all compounds where essential data are known. For instance you can find directly the measured numerical value of an IC50, a lethal dose or a spectral peak, a specific preparation method or the price and supplier address for ordering a compound. The databases are bidirectional connected to the original literature and to major reference works (electronic handbooks).
- DiscoveryGate is the gateway for getting to the scientific articles of your profession. There are only very few portals besides SciFinder and DiscoveryGate to access on-line journals via a structure/reaction search. The search engines of the journals do not allow you to search by data, for example yield.> 85%. SciFinder allows very limited numerical searches. DiscoveryGate is the only search engine to find journals that allows you a broad variety of data searches in combination with structure and reaction searches.
Reaction Searching in DiscoveryGate: We have asked Herman Skolnik Award winner Guenter Grethe (http://www.acscinf.org/cinf/awards/grethebio.htm) to prepare a lecture illustrating reaction searching using the databases and integrated Major Reference Works in DiscoveryGate. MDL Patent Chemistry Database is the first database for end-users, which provides patent reactions with their experimental reaction texts, substances with their measured data (e.g. data from bioassays, spectral peaks), prophetic compounds, and Markush structure/reaction display. We have asked Eva Seip, product manager at Elsevier MDL to illustrate how the data are organized in the Patent Chemistry Database to enable a layman to understand the claims of a patent, and to search for information that is nowhere else published. Scopus is the largest abstract and citation database of research literature and quality web sources. Scopus Citation Tracker, a new feature available to all subscribers that enables researchers to easily evaluate research using citation data. The Scopus Citation Tracker empowers researchers and librarians by providing them with a user-friendly way to more easily and efficiently check and track citation data for the purposes of gaining intelligence about articles, authors, their own published work and research trends. An interface to DiscoveryGate enables the researcher to combine text with structure/reaction searches. Access to electronic journals is automatically enabled in all MDL databases. We will explain how we can add back-issues and other items that are not on public Internet servers. MDL Notebook and Isentris, a platform and architecture to access personal, and on-line information. Imagine you scroll through reactions in your electronic lab journal and you see also the corresponding entry in CrossFire Beilstein. Imagine you choose a solvent, and your physical data from CrossFire Beilstein are added automatically. You add a starting material, and you can choose the supplier from a pop down menu. Normally you search for data, and then you use them. Imagine search and use goes in one smooth procedure. Personal Chemist Client This is an application that combines SQL databases and ISIS/Base. This is an affordable solution for managing data and structures for people that need more data flexibility than ISIS/Base can offer and cannot afford to maintain large systems like ORACLE. PASS - a program for in silico screening enables you to predict 2000 biological effects in greater than 80% probability. We have experimental verification of enrichments of compound selections by a factor of 15. This means an incredible enrichment of 1500% of finding an active compound in a pre-screened selection. Quantum is a suite of Linux and Windows software for computer-aided molecular modelling in pharmaceutics, biotechnology and related life science fields of research. For hit identification Quantum provides a possibility for flexible docking, virtual screening and rational drug design. The outstanding feature of screening a compound against several thousands of proteins of various tissues provides accurate lead selectivity tests, and ADMET predictions. Quantum tools allow the generation of combinatorial focused library designs, pKa, logP and solubility predictions. In the proteomics field Quantum has features to predict protein activity after mutations, protein-protein interactions, and protein conformational studies. Quantum technology was developed using a novel paradigm in molecular modelling by applying quantum and molecular physics instead of statistical scoring-function-like and QSAR-like methods. The key benefit of Quantum is the outstanding precision of molecular modelling and the calculations. We market a large number of chemoinformatics tools to predict and manage data. We will choose a few tools that are priced affordable for chemists at universities and at very small laboratories. Installation demonstration of DiscoveryGate and hands-on practice: Several participants will have had some experience with DiscoveryGate, either by having acquired a license recently or having taken part in the free of charge on-line evaluations. This section is for participants who want to have an on-line evaluation or had no chance to get a short introduction for using DiscoveryGate efficiently. Introductory training and hand-on practice on the MDL Patent Chemistry Database: Using mainly the CrossFire Commander software, we will train people how to work with the database. Dr. Guenter Grethe received his doctorate at the Technical University of Braunschweig (Brunswick) in Germany in 1961 for his work on the total synthesis of tetracycline antibiotics. Guenter Grethe worked as a Research Chemist at Hoffmann-LaRoche in New Jersey for many years on the total synthesis of natural products. In 1972 Professor Todd Wipke, then at Princeton University, introduced him to the use of computers in chemistry, specifically in the field of synthesis planning. This experience led Grethe to introduce early versions of MDL's MACCS and REACCS software while working at Hoffmann-La Roche. After 22 years at Hoffmann-LaRoche, Grethe moved to MDL in 1985, now a wholly owned subsidiary of the scientific publishing giant, Elsevier Science, Inc. where he was Director of Scientific Applications in the Marketing Department. His main interests are currently in reaction databases and reaction data management and he has been especially concerned with enhancing the competency of synthetic chemists in using electronic tools in their day-to-day work. Dr. Guenter Grethe was honored by the Division of Chemical Information of the American Chemical Society (ACS) with its Herman Skolnik Award for 2001. Guenter Grethe is the Chairman of the Chemical Structure Association Trust (CSA Trust). | 
