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MMDB: an ASN.1 specification for macromolecular structure
1995
Proceedings. International Conference on Intelligent Systems for Molecular Biology
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We present an exchange specification for data describing the three-dimensional structure of biological macromolecules. ...
The specification was designed for MMDB, a Molecular Modeling Database supported by the National Center for Biotechnology Information (NCBI), based on information from the Protein Data Bank (PDB). ...
The C data structure declarations ate produced automatically from the ASN.1 specification, and data item names and semantics are described fully by the MMDB specification presented here. ...
pmid:7584445
fatcat:vmnt76ozgbamrei3qw2ufvto2y
A specification for defining and annotating regions of macromolecular structures
1995
Proceedings. International Conference on Intelligent Systems for Molecular Biology
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We present a program- and machine-independent standard for annotating macromolecular structures. ...
Data encoded by this specification may be used for communicating information about structures and for exchanging it between different computer systems. ...
T.J.P.H. is supported by the MRC and ZENECX The Annmrn ASN. 1 Specification Annrmn DEFINITIONS ::= BM;IN EXPORTS Zummn;
--Figure 2 .) 1 1 1 Figure 3 . 213 some sort of default view general ( 20 , --" ...
pmid:7584468
fatcat:simxthpe65forokay6j6ddaery
GenBank
1996
Nucleic Acids Research
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An integrated retrieval system, known as Entrez, contains data from GenBank and from the major protein sequence and structural databases, as well as related MEDLINE abstracts. ...
Users may access GenBank over the Internet through the World Wide Web and through special client-server programs for text and sequence similarity searching. ...
Molecular Modeling Database (MMDB) NCBI has begun producing a database of macromolecular 3-D structure information, specifically aimed at molecular modeling research. ...
doi:10.1093/nar/24.1.1
pmid:8594554
pmcid:PMC145592
fatcat:t53zptvztjhdvcj2xs3xm4hbda
Other Structure-Based Databases
[chapter]
2005
Methods of biochemical analysis
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What_Check Detailed stereochemical quality summaries for all protein structures. ...
Part of the Whatif package. http://www.cmbi.kun.nl/gv/whatcheck/ SFCheck Validate the experimental structure factors associated with an X-ray diffraction experiment (Vaguine et al., 1999). ...
Entries in MMDB are specified using an Abstract Syntax Notation One (ASN.1; http://asn1.elibel.tm.fr/). ...
doi:10.1002/0471721204.ch11
fatcat:wxuduryxofep7fpbp7zwlwesp4
Database resources of the National Center for Biotechnology
2003
Nucleic Acids Research
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An HIV-1-specific subtyping tool uses a set of reference sequences taken from the principle HIV-1 variants. ...
For example, display formats for GenBank records include the GenBank Flatfile, FASTA, XML, ASN.1, and others. ...
doi:10.1093/nar/gkg033
pmid:12519941
pmcid:PMC165480
fatcat:dydxcilrszbt7g67rljindwu2a
Database resources of the National Center for Biotechnology Information
2006
Nucleic Acids Research
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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 ...
ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health. Conflict of interest statement. None declared. ...
The tool supports filtering by organism so that organism-specific XML files can easily be generated from the comprehensive ASN.1 FTP file. ...
doi:10.1093/nar/gkj158
pmid:16381840
pmcid:PMC1347520
fatcat:ajgh422s6nbi3o4beemsncsyzi
Database resources of the National Center for Biotechnology Information
2001
Nucleic Acids Research
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ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health. Conflict of interest statement. None declared. ...
The complete Entrez Gene data set, as well as organism-specific subsets, is available in the compact NCBI ASN.1 format on the NCBI FTP site. ...
The tool supports filtering by organism so that organism-specific XML files can easily be generated from the comprehensive ASN.1 FTP file. UniGene. ...
doi:10.1093/nar/29.1.11
pmid:11125038
pmcid:PMC29800
fatcat:mstubvho65h2noojeknidcplwi
Database resources of the National Center for Biotechnology Information
2019
Nucleic Acids Research
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The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. ...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed ...
Formatting options vary for records of different types. Display formats for GenBank records include the GenBank Flatfile, FASTA, XML, ASN.1 and others. ...
doi:10.1093/nar/gkz899
pmid:31602479
pmcid:PMC6943063
fatcat:coscu5vbd5gtnhii2uj7czx7au
Database resources of the National Center for Biotechnology Information
2000
Nucleic Acids Research
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The online version of this article has been published under an open access model. ...
For commercial re-use permissions, please contact journals.permissions@oupjournals.org. ª 2005, the authors ...
Formatting options vary for records of different types. Display formats for GenBank records include the GenBank Flatfile, FASTA, XML, ASN.1 and others. ...
doi:10.1093/nar/28.1.10
pmid:10592169
pmcid:PMC102437
fatcat:xhsgpitasrd3na5mmjgz274zcq
GenBank
1997
Nucleic Acids Research
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An integrated retrieval system, known as Entrez, incorporates data from the major DNA and protein sequence databases, along with genome maps and protein structure information. ...
MEDLINE abstracts from published articles describing the sequences are also included as an additional source of biological annotation. ...
) and Cn3D NCBI has begun distributing a database of macromolecular three-dimensional structure information, specifically aimed at molecular modeling research. ...
doi:10.1093/nar/25.1.1
pmid:9016491
pmcid:PMC146400
fatcat:44ypwiztxjawfcddaebk4zslei
Database resources of the National Center for Biotechnology Information: 2002 update
2002
Nucleic Acids Research
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The Entrez system provides search and retrieval operations for many of these databases. ...
Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB ...
The complete Gene data set, as well as organism-specific subsets, is available in the compact NCBI Abstract Syntax Notation One (ASN.1) format on the NCBI FTP site. ...
doi:10.1093/nar/30.1.13
pmid:11752242
pmcid:PMC99094
fatcat:o3wyt5y72zhzrd7usrrsl57ake
Features and development ofCoot
2010
Acta Crystallographica Section D: Biological Crystallography
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Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. ...
Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. ...
geometry and is generated as @Rð'; Þ @x 1 ¼ @Rð'; Þ @' @' @x 1 þ @Rð'; Þ @ @ @x 1 ð2Þ (and so on for each of the x, y, z positions of the atoms in the torsion). ...
doi:10.1107/s0907444910007493
pmid:20383002
pmcid:PMC2852313
fatcat:xpah64w6z5eblf4xzsyw4zsltm
Approaches to Access Biological Data Sources
[chapter]
2012
Lipoproteins - Role in Health and Diseases
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Biological sources have a large heterogeneity at different levels: Syntactic: because of the different formats for describing the content sources usually ASN.1 (formal notation for describing data transmitted ...
Figure 1 . 1 Simple schematic for a data warehouse Approaches to Access Biological Data Sources 155
Figure 2 . 2 GAV vs. ...
doi:10.5772/48740
fatcat:x5bfjcgztzaozcx2kgstma2spa
Structural Bioinformatics: From the Sequence to Structure and Function
2009
Current Bioinformatics
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For the analysis of protein-protein interactions, Voronoi tessellations are used to quantify the macromolecular interfaces. ...
The functional specificity of a protein is linked to its structure. A great section of bioinformatics deals with the prediction, analysis and visualization of protein 3D structures. ...
Searle for the critical reading of the text. Additionally we thank the reviewers for their valuable comments. ...
doi:10.2174/157489309787158170
fatcat:nnwkrprho5g4xezhajy3iib3vq
Lamprey Hemoglobin
2000
Journal of Biological Chemistry
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The results strongly support a critical role of the E helix and the AB corner in forming the subunit interface in the dimer and rule out the ␣ 1  2 model. ...
The recent x-ray crystallographic determination of the structure of deoxy lamprey Hb, reported after the completion of this work (Heaslet, H. A., and Royer, W. ...
Royer for valuable discussions, Thomas O. Baldwin for the use of laboratory facilties, David P. Giedroc for the use of an anaerobic chamber, and Wen-Yen Kao and Claire K. Riggs for providing help. ...
doi:10.1074/jbc.275.18.13517
pmid:10788466
fatcat:rlebcvfocraxdbnrcrlcrnvjda
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