Development of a cyclodextrin database using Chemaxon tools Eszter Hazai Virtua Drug, Budapest, Hungary.

Slides:



Advertisements
Similar presentations
February 2013 Szilárd Dóránt Scientific & technical Presentation Pipeline Pilot Integration.
Advertisements

Virtual Synthesis - Reactor
In Silico Primer Design and Simulation for Targeted High Throughput Sequencing I519 – FALL 2010 Adam Thomas, Kanishka Jain, Tulip Nandu.
Polska Infrastruktura Informatycznego Wspomagania Nauki w Europejskiej Przestrzeni Badawczej Institute of Computer Science AGH ACC Cyfronet AGH The PL-Grid.
May, 2008 Presenting: Szabolcs Csepregi The ChemAxon Markush project overview and development discussion.
Scientific & technical presentation Fragmenter Nóra Máté Sept 2005.
Integrating ChemAxon technology into your End User Applications Java solutions for cheminformatics Ver. Mar., 2005.
Scientific & technical presentation Calculator Plugins January 2011.
Java Solutions for Cheminformatics Feb 2008 Whats new for PP.
Version 5.3, April 2010 The ChemAxon Markush project overview and development discussion.
Calculator Plugins József Szegezdi, Nóra Máté. ChemAxon Calculator Plugins ChemAxons plugin handling mechanism provides a framework for calculating various.
Scientific & technical presentation Standardizer January 2008.
Chemical Naming Daniel Bonniot, PhD October 2008.
Nov 2008 Scientific & technical presentation JChem for Excel.
Pipeline Pilot Integration Szilard Dorant Solutions for Cheminformatics.
SOMA2 – Drug Design Environment. Drug design environment – SOMA2 The SOMA2 project Tekes (National Technology Agency of Finland) DRUG2000 program.
Java Solutions for Cheminformatics June 2006 Conformer generation.
ChemAxon - Pipeline Pilot Integration
CONFIDENTIAL INFORMATION KnowTox, a Franco- Hungarian collaborative project relative to toxicity.
UGM, June, 2007 Szabolcs Csepregi Markush: Whats new, development discussions.
Java Solutions for Cheminformatics Structure based predictions – new plugins Zsolt Mohácsi, Nóra Máté, József Szegezdi, Ödön Farkas, Gábor Imre, Imre Jákli.
SEURAT Structure Exploration Utility for RAtional Therapeutics ChemAxon US UGM– September 2009.
1 Miklós Vargyas, Judit Papp May, 2005 MarvinSpace – live demo.
Name to structure, Structure to name, chemicalize.org Daniel Bonniot de Ruisselet Solutions for Cheminformatics.
2008 Accelrys EUGM Pipelining ChemAxon Szilard Dorant Solutions for Cheminformatics.
Java Solutions for Cheminformatics March About Us Molecule Drawing and Visualization Structure Searching Cartridge Structure Standardization Molecular.
Solutions for Cheminformatics
Chapter 8 Sections 2 and 3 Chapter 4 Section 5. Monomers- smaller molecules that join together to make polymers.
Mobile Distillery – Technical Session 16 Technical Session 16 At the Heart of Parametric Development by Razmig Sarkissian CTO.
Query Manager. QM is a collection of tools you can use to obtain information from the AS/400 database Used to –select, arrange, and analyze information.
Manufacturing Knowledge Management Sep Sep 2010 Manufacturing Knowledge Warehouse Development Investigator: Asmaa Alabed Supervisor: Xun Chen Industrial.
University of Leeds Department of Chemistry The New MCM Website Stephen Pascoe, Louise Whitehouse and Andrew Rickard.
About ISoft … What is Decision Tree? Alice Process … Conclusions Outline.
In Silico Design of Selective Estrogen Receptor Modulators from Triazoles and Imines Joey Salisbury Dr. John C. Williams Small Molecules/Large Molecules.
Computational Chemistry. Overview What is Computational Chemistry? How does it work? Why is it useful? What are its limits? Types of Computational Chemistry.
Information Need Question Understanding Selecting Sources Information Retrieval and Extraction Answer Determina tion Answer Presentation This work is supported.
Introduction to Chemoinformatics Irene Kouskoumvekaki Associate Professor December 12th, 2012 Biological Sequence Analysis course.
A unifying model of cation binding by humic substances Class: Advanced Environmental Chemistry (II) Presented by: Chun-Pao Su (Robert) Date: 2/9/1999.
Cyclodextrin.
AMBIT Chemoinformatics Software for Data Management Joanna Jaworska Nina Jeliazkova P&G Brussels, Ideaconsult Ltd., Belgium Bulgaria.
Writing Scientific Papers Additional materials required for manuscript preparation and submission Prof Steve Leharne.
Open source software and web services for designing therapeutic molecules G. P. S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology,
In silico discovery of inhibitors using structure-based approaches Jasmita Gill Structural and Computational Biology Group, ICGEB, New Delhi Nov 2005.
1 Cheminformatics David Shiuan Department of Life Science and Institute of Biotechnology National Dong Hwa University.
Modular Approach To Modeling Of The Apoptosis Machinery E. O. Kutumova 1,2,*, R. N. Sharipov 1,3,2, F. A. Kolpakov 1,2 1 Institute of Systems Biology,
Meta-analysis Overview
FLUKA dose and fluence simulations for CBM experiment I.Kadenko, O.Bezshyyko, V.Pluyko, V.Shevchenko National Taras Shevchenko University of Kiev.
EndNote: The Next Steps Rebecca Starkey Reference Librarian The Joseph Regenstein Library
W e present BiNoM [1,2], a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats.
Pathway: a collection of genes, proteins, and /or small molecules that modulate a cellular process or disease state Growing demand in biological sciences.
Chapter 2 A systems view of project management. Learning objectives apply systems theory to explain the interrelations between project elements discuss.
While gene expression data is widely available describing mRNA levels in different cancer cells lines, the molecular regulatory mechanisms responsible.
Lets Carb Up!!!. Carbohydrates - Composition Made of… (Hint: look at the name) Carbon Hydrogen Oxygen.
Introduction to Chemoinformatics and Drug Discovery Irene Kouskoumvekaki Associate Professor February 15 th, 2013.
Taming the Big Data in Computational Chemistry #euroCRIS2015 Barcelona 9-11-XI-2015 Carles Bo ICIQ (BIST) -
Development of a Signaling Pathway Map for the FXM Gil Sambrano, Lily Jiang, Madhu Natarajan, Alex Gilman, Adam Arkin University of California San Francisco,
Développement "IN SILICO" de nouveaux extractants et complexants de métaux Alexandre Varnek Laboratoire d’Infochimie, Université Louis Pasteur, Strasbourg,
AV-EMS: Development of an Emergency Management Software Application Using ArcView Nick Stadnyk, GIS Program Manager - Applied Data Consultants, Inc. Matt.
Docking and Virtual Screening Using the BMI cluster
COMPLEXATION WITH BETACYCLODEXTRINS IMPROVE STABILITY AND SOLUBILITY OF DRUGS IN DOSAGE FORMS قحطان جاسم حسون.
3. Results and Discussion 2. Computational Methods
Profiling based unstructured process logs
Macromolecules Database Creation for Polymer Properties
KDD CUP 2001 Task 1: Thrombin Jie Cheng (
DIGITAL LIBRARY.
Runs, Parameter Sets, Outputs and Projects
Extracting Recipes from Chemical Academic Papers
Business Intelligence
Copyright © Allyn & Bacon 2006
Presentation transcript:

Development of a cyclodextrin database using Chemaxon tools Eszter Hazai Virtua Drug, Budapest, Hungary

Why Cyclodextrins? Definition: Cyclodextrins (CDs) are cyclic oligosaccharides obtained by the enzymatic conversion of starch. α-cyclodextrin: six sugar ring molecule β-cyclodextrin: seven sugar ring molecule γ-cyclodextrin: eight sugar ring molecule Cyclodextrins and drugs ( ): 1800 CD-drug paper 715 patent About 30 drugs, e.g. Cetirizine-BCD (Cetirizin) Diclofenac-BCD (Voltaren ophtha) Omeprazole-BCD (Omebeta)

Why Database? Database in general Integrate current knowledge on a specific research area Aimed at bringing together information from diverse source Provide easy and fast way for data mining Our aim at creating cyclodextrin database Relatively few experimental conditions in order to give a quick, rough overview on cyclodextrin binding– if you need every data, read the paper Data collected- should be used for prediction as well

3 modules: Literature – all general data Interaction – extracted structural data Prediction – in silico prediction methods

Cyclodextrin database

Literature module

Cyclodextrin database Interaction module

Cyclodextrin database Prediction module

Prediction module: Parameters influencing cyclodextrin complexation have been explored – in silico prediction with high prediction rate Why Chemaxon? cxcalc input.mol majorms -H 2.0 -f smiles > output.smi # 2-es pH a 2.0 molconvert -3:c30[hydrogenize] mol input.smi -o output.mol Or: molconvert -3:c2[hydrogenize] mol input.mol -o output.mol Molecular modelling – plenty of file formats (Babel) Protonation at a given pH? Smiles to 3D conversion? Chemaxon Calculator Plugins