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Online Predicted Human Interaction Database

K. R. Brown, I. Jurisica
2005 Bioinformatics  
Results: The Online Predicted Human Interaction Database (OPHID) is a web-based database of predicted interactions between human proteins.  ...  The 23 889 predicted interactions currently listed in OPHID are evaluated using protein domains, gene co-expression and Gene Ontology terms.  ...  these databases only recapitulate the known interactions published in the literature.  ... 
doi:10.1093/bioinformatics/bti273 pmid:15657099 fatcat:fsppzovlhnd33hvf5iklnilnaq

CRISPI: a CRISPR interactive database

C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas
2009 Bioinformatics  
ACKNOWLEDGEMENTS The necessary environment for all computations has been provided by the bioinformatics platform Biogenouest ( Funding: This work is supported by a grant from the  ...  Access the CRISPI database The main page of CRISPI offers three search forms: consult the content of the database, Blast a personal sequence against the database and find CRISPR structures in a personal  ...  The Blast results pages are cross-linked with the CRISPI database so that it is easy to return to the database by clicking on hyperlinks.  ... 
doi:10.1093/bioinformatics/btp586 pmid:19846435 pmcid:PMC2788928 fatcat:efy5oybvk5cfzi6yhbnnzvbyhu

IMID: integrated molecular interaction database

S. Balaji, C. Mcclendon, R. Chowdhary, J. S. Liu, J. Zhang
2012 Bioinformatics  
IMID allows complex and versatile queries for context-specific molecular interactions, which are not available currently in other molecular interaction databases.  ...  However, most databases focus on only one type of interactions, which are often not well annotated and integrated with related functional information.  ...  Overall, our database has several unique features compared with other databases: (1) The interactions in the database are linked to their biological context represented by various biological terms.  ... 
doi:10.1093/bioinformatics/bts010 pmid:22238258 pmcid:PMC3289914 fatcat:2vaxtiswwfarnomq4ahlliopzi

SPiD: a subtilis protein interaction database

M. Hoebeke, H. Chiapello, P. Noirot, P. Bessieres
2001 Bioinformatics  
Bioinformatics tools are needed to perform this graph visualization while maintaining a link to the experimental data.  ...  Graph-like structures emerging from the accumulation of interaction data make it difficult to maintain a consistent and global overview by hand.  ...  She made significant contributions to the database contents, and was actively involved in program specifications and user interface design issues.  ... 
doi:10.1093/bioinformatics/17.12.1209 pmid:11751229 fatcat:mfmni77iwva2zbqgmcek5otrg4

HPID: The Human Protein Interaction Database

K. Han, B. Park, H. Kim, J. Hong, J. Park
2004 Bioinformatics  
The Human Protein Interaction Database (http:// was designed (1) to provide human protein interaction information pre-computed from existing structural and experimental data, (2) to predict  ...  For each human protein in the database and each query submitted by users, the protein superfamilies and yeast proteins assigned to the protein are shown, along with their interacting partners.  ...  Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.  ... 
doi:10.1093/bioinformatics/bth253 pmid:15117749 fatcat:226rstknfje4njicztetpvoyma

Interactive data input into the GeneNet database

F. A. Kolpakov, E. A. Ananko
1999 Bioinformatics  
The GeneNet database has been developed for a formalized hierarchical description of the gene networks.  ...  To provide rapid data accumulation in the database, the Java graphical interface for data input through the Internet by independent experts equipped with convenient visual tools is developed.  ...  An object-oriented database GeneNet (Kolpakov et al., 1998) was developed for accumulating these data.  ... 
doi:10.1093/bioinformatics/15.7.713 pmid:10487877 fatcat:dzhm6haemzcoxh4jo33fe5rpjq

SPIDer: Saccharomyces protein-protein interaction database

Xiaomei Wu, Lei Zhu, Jie Guo, Cong Fu, Hongjun Zhou, Dong Dong, Zhenbo Li, Da-Yong Zhang, Kui Lin
2006 BMC Bioinformatics  
The database is accessible at http:// Conclusion: SPIDer is a public database server for protein-protein interactions based on the yeast genome.  ...  It also provides general links to connect predicted protein-protein interactions with three other databases, DIP, BIND and MIPS.  ...  (page number not for citation purposes) SGD: Saccharomyces Genome Database DIP: Database of Interacting Proteins BIND: Biomolecular Interaction Network Database MIPS: Munich Information Center for  ... 
doi:10.1186/1471-2105-7-s5-s16 pmid:17254300 pmcid:PMC1764472 fatcat:l3c3cynftzacnigteurwmf4iqa

4DGenome: a comprehensive database of chromatin interactions

Li Teng, Bing He, Jiahui Wang, Kai Tan
2015 Bioinformatics  
Results: We describe the 4DGenome database that stores chromatin interaction data compiled through comprehensive literature curation.  ...  Records in the database are described using a standardized file format, facilitating data exchange. The vast major of the interactions were assigned a confidence score.  ...  This file format is similar to formats used by many protein-protein interaction databases, such as the BioGrid (Chatr-Aryamontri et al., 2013) database.  ... 
doi:10.1093/bioinformatics/btv158 pmid:25788621 pmcid:PMC4514924 fatcat:457an7nmdzcjtly2tg3ffihzum

Integrated web visualizations for protein-protein interaction databases

Fleur Jeanquartier, Claire Jean-Quartier, Andreas Holzinger
2015 BMC Bioinformatics  
Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery.  ...  However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks.  ...  of the Bioinformatics resource MINT.  ... 
doi:10.1186/s12859-015-0615-z pmid:26077899 pmcid:PMC4466863 fatcat:zgaaf7hwnbap5ayondw3eqqhgu

COPS Benchmark: interactive analysis of database search methods

K. Frank, M. Gruber, M. J. Sippl
2010 Bioinformatics  
The performance of sequence database search methods is usually judged by receiver operating characteristic (ROC) analysis.  ...  Here we provide a standardized dataset, called COPS-Benchmark 2009/6, derived from the classification of protein structure (COPS) database (Suhrer et al., 2009) .  ...  Hence, the server is a useful tool for a wide range of problems encountered in bioinformatics, and in particular for algorithm developers and for all users who need to understand the range of applicability  ... 
doi:10.1093/bioinformatics/btp712 pmid:20080504 fatcat:qqgppcrm6bdsleeyqfzmo6bnue

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick, George Magklaras, Ian M Donaldson
2008 BMC Bioinformatics  
Interaction data for a given protein may be spread across multiple databases.  ...  Our method required that we map protein database references found in interaction records to current protein sequence records.  ...  Background Protein interaction data are an increasingly important bioinformatics dataset used in biomedical research.  ... 
doi:10.1186/1471-2105-9-405 pmid:18823568 pmcid:PMC2573892 fatcat:vsv6fbiizbaf7n6x3z6fsxvbcm

NPIDB: a Database of Nucleic Acids Protein Interactions

S. Spirin, M. Titov, A. Karyagina, A. Alexeevski
2007 Bioinformatics  
The database NPIDB (Nucleic Acids-Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from PDB (1834 complexes in July 2007).  ...  The content of the database is weekly updated.  ...  acid-protein interaction.  ... 
doi:10.1093/bioinformatics/btm519 pmid:17977883 fatcat:kvr2nr6k5jf6poid7zzhv45oa4

A protein domain interaction interface database: InterPare

Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak
2005 BMC Bioinformatics  
We introduce a large-scale protein domain interaction interface database called InterPare  ...  InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known.  ...  We also thank all the scientists in the field of protein-protein interaction.  ... 
doi:10.1186/1471-2105-6-207 pmid:16122378 pmcid:PMC1236910 fatcat:xg2belho5vdv7cq4fmn2326tua

The MIPS mammalian protein-protein interaction database

P. Pagel, S. Kovac, M. Oesterheld, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, P. Mark, V. Stumpflen, H.-W. Mewes, A. Ruepp, D. Frishman
2004 Bioinformatics  
The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals.  ...  Availability: The MPPI database is located at proj/ppi/ Contact:  ...  ACKNOWLEDGEMENTS We would like to thank Ulrich Güldener and Martin Münsterkötter from the MIPS yeast database group and Philip Wong for helpful comments.  ... 
doi:10.1093/bioinformatics/bti115 pmid:15531608 fatcat:rn6vfarvtra53du4tdiaw6alvy

Thermodynamic database for protein-nucleic acid interactions (ProNIT)

P. Prabakaran, J. An, M. M. Gromiha, S. Selvaraj, H. Uedaira, H. Kono, A. Sarai
2001 Bioinformatics  
Compounding the issue is a poor database correlating wildlife diversity and abundance with varying levels of dead wood, and hence, a lack of basic information on which to base reliable dead wood goals  ... 
doi:10.1093/bioinformatics/17.11.1027 pmid:11724731 fatcat:q7loyziucfbwtgjqetp5j2kaaq
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