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Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

George Nicola, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson
2015 Database: The Journal of Biological Databases and Curation  
Connecting proteins with drug-like compounds: open source drug discovery workflows with BindingDB and KNIME.  ...  Abstract Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration.  ...  One may then display the results by selecting the MarvinView node's Execute and Open Views option.  ... 
doi:10.1093/database/bav087 pmid:26384374 pmcid:PMC4572361 fatcat:tytczenu5jbrjesokdnktmuhe4

MOESM1 of Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
2018 Figshare  
Additional file 1. List of automatic changes performed by the fixalot script and examples of COD entries with wrong compound names in the CIF.
doi:10.6084/m9.figshare.6289739.v1 fatcat:r2ic5t6ov5gjbmyex7sfzuxmgm

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys, Antanas Vaitkus
2018 Journal of Cheminformatics  
In this article, the ongoing work to describe the chemical connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported.  ...  Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure.  ...  Conclusions Work has been started to extract the chemical connectivity from entries contained in the Crystallography Open Database.  ... 
doi:10.1186/s13321-018-0279-6 pmid:29777317 pmcid:PMC5959826 fatcat:wjzzshyefbetdm6ogqug4wtwji

A New Design for Open and Scalable Collaboration of Independent Databases in Digitally Connected Enterprises

David Levermore, Gilbert Babin, Cheng Hsu
2010 Journal of the AIS  
An open and scalable design for connecting the manufacturer's enterprise databases to any supply chains is required. The ideal is not yet reality.  ...  In general, open and scalable connection of databases supports an enterprise to simultaneously participate, on demand, in many collaboration relations across many supply chains, as the manufacturer in  ...  NEW INFORMSTION SYSTEM DESIGNS FOR NEW BUSINESS DESIGNS: A DIGITAL CONNECTION PERSPECTIVE I.1 Design Goals: Open and Scalable Connection of Independent Databases Examples of digitally connected enterprises  ... 
doi:10.17705/1jais.00233 fatcat:qasd5rsqmbbd7itt3kbp7eiv6m

Systematic polypharmacology and drug repurposing via an integrated L1000-based Connectivity Map database mining

Tsang-Pai Liu, Yao-Yu Hsieh, Chia-Jung Chou, Pei-Ming Yang
2018 Royal Society Open Science  
The Connectivity Map (CMap) is a database collecting gene-expression profiles of drug-treated human cancer cells, which has been widely used for investigation of polypharmacology and drug repurposing.  ...  Large-scale databases have been accumulated in recent years, and utilization and integration of these databases would be highly helpful for polypharmacology and drug repurposing.  ...  The Connectivity Map (CMap) is a database that collects microarray-based gene-expression profiles from cultured human cancer cell lines treated with various experimentally and clinically used small molecules  ... 
doi:10.1098/rsos.181321 pmid:30564416 pmcid:PMC6281908 fatcat:6ytrj2efyvaizojdum6kdpyssi

Application of open-access databases to determine functional connectivity between resveratrol-binding protein QR2 and colorectal carcinoma

Barbara B. Doonan, Evelien Schaafsma, John T. Pinto, Joseph M. Wu, Tze-chen Hsieh
2017 In vitro Cellular & Developmental Biology-Animal  
Application of open-access databases to determine functional connectivity between resveratrol-binding protein QR2 and colorectal carcinoma.  ...  We hypothesize that the relationship between resveratrol and different CRC etiologies might be gleaned using publicly available databases.  ...  The Oncomine database is available both as a subscription database and as open access.  ... 
doi:10.1007/s11626-017-0174-x pmid:28646291 fatcat:qbqiul3wk5e4fknqcj3vo5mm5e

A Common Database and a Transaction Pool to Reduce Data Redundancy and to Maximize Database Throughput in a Comprehensive Information System of a Particular Domain of Interests

Mohammad Ghulam Ali, Mohammad Ghulam Murtuza
2011 Journal of clean energy technologies  
We also illustrate some examples of a transaction pool to connect transaction databases with a common database. We have also illustrated how to create non-visual transaction objects within the system.  ...  The transaction pool will reduce the number of times new connection objects are created, will promote connection object reuse, will quicken the process of getting a connection and will control the amount  ...  Instead, the database connections are kept open in the transaction pool so that they can be reused for other database operations.  ... 
doi:10.7763/ijcte.2011.v3.380 fatcat:qdlypqyh3nbnja3zosya533ifu

Wikidata for 5-star Linked Open Databases: A case study of PanglaoDB

Tiago Lubiana, João Vitor Ferreira Cavalcante
2021 Zenodo  
Wikidata for 5-star Linked Open Databases: A case study of PanglaoDB Overview: • PanglaoDB is a database of cell type markers • Data in PanglaoDB is available in tables, but not as linked data • Wikidata  ...  Connecting data to Wikidata fullfills all criteria. More information about 5-star Linked Open Data here)  ... 
doi:10.5281/zenodo.5747848 fatcat:f3op4n5q7vg33iniqljevwrkpq

Database of open-framework aluminophosphate structures

Chuting Zheng, Yi Li, Jihong Yu
2020 Scientific Data  
This database will provide important insight into understanding the structural chemistry of open-framework aluminophosphate compounds.  ...  We have collected 312 open-framework aluminophosphate crystal structures from published literature and established a database for these structures.  ...  Fig. 2 2 Fig. 2 All possible polyhedral connectivity observed in open-framework aluminophosphate database.  ... 
doi:10.1038/s41597-020-0452-4 pmid:32235834 fatcat:h6iqqqk4znfmzgrlqzmy537kl4

GIS Open Source Application as a Support to a Hospital Morbidity Database - Hospital GIS

Lia Duarte, Ana Cláudia Moreira Teodoro, Alberto Freitas
2017 Proceedings of the 3rd International Conference on Geographical Information Systems Theory, Applications and Management  
This data was previously added to PostGIS (an open source database) and automatically connected to the application.  ...  The large amount of data requires the connection to a free database in GIS environment enhancing the practical applicability, rapid, safe and efficient data representation.  ...  Then the database connection is performed and consequently opens.  ... 
doi:10.5220/0006268901690176 dblp:conf/gistam/DuarteTF17 fatcat:6occixyjzrdobirapbjx25nx3i

Designing a Virtual Center for E-Commerce

Doina ROSCA, Logica BANICA
2010 Annals of Dunarea de Jos University. Fascicle I : Economics and Applied Informatics  
database servers of the companies that offer e-commerce sevices and also to interract with electronic payment and e-administration systems.  ...  This paper presents the current stage of the experimental system design and implementation, an open system website-based (called Single Way for E-Commerce - SWEC) having the goal to collaborate with many  ...  The actual researches are focuses on opening databases of different structure using corresponding languages by the means of an ODBC connection (ODBC -Open Database Connectivity).  ... 
doaj:aa0aa43362694bdbaee2eb8939b6ac18 fatcat:jxiuh4ic7nbpjcboclxjiipfeq


Alok Bajpai .
2015 International Journal of Research in Engineering and Technology  
Database, XML Database and Oracle Server Database.  ...  Database management system is a software application that interacts with the user and the database itself to capture and analyze data.  ...  no data provider ofthe given databases then the user can't open database file.  ... 
doi:10.15623/ijret.2015.0422003 fatcat:jqwc7q2xx5cr3f2ngaiwccgyve

Page 68 of Library & Information Science Abstracts Vol. , Issue 10 [page]

1993 Library & Information Science Abstracts  
with - Bibliographic records 6547 Connected with - Business information - Information work 6515 Connected with - Civil engineering 6824 Connected with - Computer science 6731 Connected with - Networks  ...  6643 Open Source Solutions Inc.  ... 

Database for the semi-rigid behaviour of beam-to-column connections in seismic regions

P.J.S Cruz, L.A.P Simões da Silva, D.S Rodrigues, R.A.D Simões
1998 Journal of constructional steel research  
Simplified constitutive models for the hysteretic behaviour of connections are presented and included in the database for comparison and calibration with experimental results.  ...  burden of carrying out experimental work, avoiding being misled by incomplete or incorrect data, and opening the way to design assisted by testing.  ...  All rights reserved KEYWORDS Database, steel connections, composite connections, semi-rigid connections, beam-to-column connections.  ... 
doi:10.1016/s0143-974x(98)80023-0 fatcat:azn3qi4tjvenreuf6hvdid7yau

Page 130 of Library & Information Science Abstracts Vol. , Issue 9 [page]

1995 Library & Information Science Abstracts  
Open Document Architecture Software - Multimedia - Online databases: 10787 learning nim toe instruction: 11085 Students - User needs - Libraries: 10208 Open learning see also Distance learning Open Library  ...  Network, Netherlands: 10340 Open Market: 10846 systems CD-ROM databases - Use for - Searching - Holdings statements - Periodicals - Online catalogues: 10650 Open Systems Interconnection Electronic media  ... 
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