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          Institute: MPI für molekulare Physiologie     Collection: Abteilung IV - Chemische Biologie     Display Documents

ID: 429252.0, MPI für molekulare Physiologie / Abteilung IV - Chemische Biologie
Interactive Exploration of Chemical Space with Scaffold Hunter
Authors:Wetzel, Stefan; Klein, Karsten; Renner, Steffen; Rauh, Daniel; Oprea, Tudor I.; Mutzel, Petra; Waldmann, Herbert
Research Context:Cheminformatics
Date of Publication (YYYY-MM-DD):2009-06-28
Title of Journal:Nature Chemical Biology
Issue / Number:8
Start Page:581
End Page:583; 696
Sequence Number of Article:1
Review Status:Peer-review
Audience:Experts Only
Intended Educational Use:Yes
Abstract / Description:The supporting information is composed of the following files:

I. pyruvatekinasedata.zip

The pyruvate kinase data set used for the analysis described in the referenced publication is contained in this file. The analysis is based on the Pyruvate Kinase Screen as published in PubChem under the assay ID 361. It contains all compounds checked in this screen together with the scaffold tree generated from it. Scaffold Hunter can be used to query the database and interactively display the scaffold tree. This file is a dump from a MySQL 5.1 database and was generated with MySQL Administrator 1.2.5. It can be restored with the same program.

II. scaffoldhunter_profiles.zip

Scaffold Hunter saves the user profiles either on the hard disk or in a database. The corresponding database schema is contained in this zip file. This schema must be contained in the MySQL database before Scaffold Hunter can be run. This file is a dump from a MySQL 5.1 database and was generated with MySQL Administrator 1.2.5. It can be restored with the same program.

III. InstallationGuide_Databases.pdf

This document describes the installation of a local MySQL database server and the graphical user interface MySQL Administrator. Restoration of the profiles and sample databases are also described.

IV. run_ScaffoldHunter.bat

Windows batch file to run Scaffold Hunter with 1024 MByte of Memory.

V. run_ScaffoldTreeGenerator.bat

Windows batch file to run ScaffoldTreeGenerator with 1024 MByte of Memory.

VI. ScaffoldHunter_readme.txt

Textfile with advice for the installation of Scaffold Hunter.

VII. ScaffoldTreeGenerator_readme.txt

Textfile with advice for the installation of ScaffoldTree Generator.
External Publication Status:published
Document Type:Article
Communicated by:Jürgen Block
Affiliations:MPI für molekulare Physiologie/Abteilung IV - Chemische Biologie/AG Prof. Dr. Herbert Waldmann
MPI für molekulare Physiologie/Chemical Genomics Center of the MPS /AG Dr. Daniel Rauh
External Affiliations:Chemical Biology, Technical University of Dortmund, D-44227 Dortmund, Germany;
Chair of Algorithm Engineering, Faculty of Computer Sciences, Technical University Dortmund, Otto-Hahn-Str. 14, D-44227 Dortmund, Germany;
University of New Mexico School of Medicine, Division of Biocomputing, MSC11 6145, Research Incubator Building, Suite 170, 2703 Frontier, NE, 1 University of New Mexico, Albuquerque, NM 87131, United States of America
Relations:Has References-URL:http://sourceforge.net/projects/scaffoldhunter/ [Project Homepage]
Has References-URL:http://www.scaffoldhunter.de/ [Project Homepage]
Identifiers:URL:http://dx.doi.org/10.1038/nchembio.187 [article locator with full text links]
Full Text:
You have privileges to view the following file(s):
pyruvatekinasedata.zip  [208,00 Mb] [Comment:application/zip]  
scaffoldhunter_profiles.zip  [1,00 Kb] [Comment:application/zip]  
InstallationGuide_Databases.pdf  [1,00 Mb] [Comment:pdf file]  
run_ScaffoldHunter.bat  [39 b] [Comment:windows batch file]  
run_ScaffoldTreeGenerator.bat  [46 b] [Comment:windows batch file]  
ScaffoldHunter_readme.txt  [1,00 Kb] [Comment:Textfile]  
ScaffoldTreeGenerator_readme.txt  [1,00 Kb] [Comment:Textfile]  
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