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HIV-1, human interaction database: current status and new features

Danso Ako-Adjei, William Fu, Craig Wallin, Kenneth S. Katz, Guangfeng Song, Dakshesh Darji, J. Rodney Brister, Roger G. Ptak, Kim D. Pruitt
2014 Nucleic Acids Research  
The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Interaction Database', available through the National Library of Medicine at http://www.ncbi.nlm.nih.gov/genome/viruses/ retroviruses/hiv-1/interactions  ...  In addition to specific HIV-1 protein-human protein interactions, included are interaction effects upon HIV-1 replication resulting when individual human gene expression is blocked using siRNA.  ...  Michael Inskeep and Ms. Erika Maynor for their efforts in reviewing and editing interaction descriptions, and Dr.  ... 
doi:10.1093/nar/gku1126 pmid:25378338 pmcid:PMC4383939 fatcat:3274ywi5i5bmrb4luchga6xtie

The Molecular Biology Database Collection: an updated compilation of biological database resources

A. D. Baxevanis
2001 Nucleic Acids Research  
The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches.  ...  and expression data PROMISE http://bioinf.leeds.ac.uk/promise/ Prosthetic centers and metal ions in protein active sites Peptaibol  ...  HIV Sequence Database http://hiv-web.lanl.gov/ HIV RNA sequences Human BAC Ends Database http://www.tigr.org/tdb/humgen/bac_end_search/ bac_end_intro.html Non-redundant human BAC end sequences  ... 
doi:10.1093/nar/29.1.1 pmid:11125037 pmcid:PMC29860 fatcat:t7pctxvehncsfliq6a4nywqx5u

The Molecular Biology Database Collection: 2002 update

A. D. Baxevanis
2002 Nucleic Acids Research  
The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches.  ...  Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http:// nar.oupjournals.org.  ...  / Information regarding complete and ongoing genome projects HERV http://herv.img.cas.cz/ Human endogenous retroviruses HIV Sequence Database http://hiv-web.lanl.gov/ HIV RNA sequences HOWDY  ... 
doi:10.1093/nar/30.1.1 pmid:11752241 pmcid:PMC99169 fatcat:n46iu5l6oreapd5yxswe7pmg5m

The Molecular Biology Database Collection: 2003 update

A. D. Baxevanis
2003 Nucleic Acids Research  
The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches.  ...  Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at  ...  I also wish to thank Debbie Wilson and Karen Otto for providing logistical support and for their assistance in tracking and processing the manuscripts that appear in this issue.  ... 
doi:10.1093/nar/gkg120 pmid:12519937 pmcid:PMC165567 fatcat:kbq66plg3rdkppl5tqqwfu7pue

Other Structure-Based Databases [chapter]

Helge Weissig, Philip E. Bourne
2005 Methods of biochemical analysis  
Includes those listed above in this table. http://pdb.rutgers.edu/validate/ Protein-protein interaction server  ...  PDB validation server Validate the format and content of a PDB entry using the same software procedures as used by the PDB.  ...  HIV Proteases-http://mcl1.ncifcrf.gov/hivdb/index.html The HIV Protease Database (HIVdb) archives experimentally determined structures of human immunodeficiency virus 1 (HIV1), human immunodeficiency virus  ... 
doi:10.1002/0471721204.ch11 fatcat:wxuduryxofep7fpbp7zwlwesp4

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+31 others)
2011 Nucleic Acids Research  
PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and  ...  chemicals (Biosystems and the Pub-Chem suite of small molecule databases).  ...  HIV-1/human protein interaction database The HIV-1/Human Protein Interaction Database is an online presentation of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins  ... 
doi:10.1093/nar/gkr1184 pmid:22140104 pmcid:PMC3245031 fatcat:zxmwupa435gfzcpusnv7oe3qnm

TB database: an integrated platform for tuberculosis research

T. B. K. Reddy, R. Riley, F. Wymore, P. Montgomery, D. DeCaprio, R. Engels, M. Gellesch, J. Hubble, D. Jen, H. Jin, M. Koehrsen, L. Larson (+11 others)
2009 Nucleic Acids Research  
ACKNOWLEDGEMENTS We are grateful to the research community for their valuable input and suggestions in building and maintaining this database.  ...  TB is today the second highest cause of death from infectious diseases after HIV/AIDS (1) and is the biggest killer of people infected with HIV (2) .  ...  new drugs, vaccines and biomarkers.  ... 
doi:10.1093/nar/gkn652 pmid:18835847 pmcid:PMC2686437 fatcat:6v7xu5kscjhxnadfuspg42jxsa

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer (+21 others)
2009 Nucleic Acids Research  
A new Advanced Search option is available that reorganizes the current Limits and Preview/Index  ...  Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases.  ...  HIV-1/Human Protein Interaction Database.  ... 
doi:10.1093/nar/gkn741 pmid:18940862 pmcid:PMC2686545 fatcat:wbtxaka7ibbbdn7xj2ga7n46ge

The Biomolecular Interaction Network Database in PSI-MI 2.5

Ruth Isserlin, Rashad A. El-Badrawi, Gary D. Bader
2011 Database: The Journal of Biological Databases and Curation  
Databases that incorporate a specific subset of BIND data include Human Annotated and Predicted Protein Interaction (HAPPI) (8) , Human Protein Interaction Database (HPID) (9) and UniHI (10) for human  ...  STRING (17) , Human Protein-Protein Interaction Prediction (PIPS) (18) and Interologous Interaction Database (I2D) (19) collect and predict interactions and include BIND as an interaction source.  ...  Supplementary Data Supplementary data are available at Database Online. Conflict of interest. None declared.  ... 
doi:10.1093/database/baq037 pmid:21233089 pmcid:PMC3021793 fatcat:pxyrbatim5adrfa3n5skdl3v74

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  PROTEINS HIV-1/Human Protein Interaction Database.  ...  HIV Protein-Interaction Database of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins or proteins from disease organisms associated with HIV or AIDS (16).  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  PROTEINS HIV-1/Human Protein Interaction Database.  ...  HIV Protein-Interaction Database of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins or proteins from disease organisms associated with HIV or AIDS (16).  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L. Y. Geer (+21 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and  ...  HIV-1/Human Protein Interaction Database.  ...  HIV Protein-Interaction Database of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins or proteins from disease organisms associated with HIV or  ... 
doi:10.1093/nar/gkm1000 pmid:18045790 pmcid:PMC2238880 fatcat:geht7s3fgnguvnvfnga5kd2zmq

Database resources of the National Center for Biotechnology Information

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer (+28 others)
2009 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  HIV-1/Human Protein Interaction Database.  ...  HIV Protein-Interaction Database of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins or proteins from disease organisms associated with HIV or AIDS (56) .  ... 
doi:10.1093/nar/gkp967 pmid:19910364 pmcid:PMC2808881 fatcat:duzfi6ea4rdvvb5wbhr7z2mbpq

Curated databases and their role in clinical bioinformatics

C.C. Englbrecht, M. Han, M.T. Mader, A. Osanger, K.F.X. Mayer
2004 IMIA Yearbook of Medical Informatics  
Status of the Human Genome The sequences of human and other organisms represent fundamental information for biology and biomedicine.  ...  Table 1 . 1 Selected Collection of curated and regularly updated Molecular Biological Databases.  ...  The Comprehensive Microbial Resources http://www.tigr.org/tdb/ http://www.sanger.ac.uk/Projects/Microbes Microbial sequence and annotation database [110] HIV Sequence Database http://hiv-web.lanl.gov  ... 
doi:10.1055/s-0038-1638188 fatcat:ziahknl6kjdu7jz5oabyvtvbui
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