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MMDB: an ASN.1 specification for macromolecular structure

H Ohkawa, J Ostell, S Bryant
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
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

S E Brenner, T J Hubbard
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
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

D. Benson
1996 Nucleic Acids Research  
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]

Helge Weissig, Philip E. Bourne
2005 Methods of biochemical analysis  
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

D. L. Wheeler
2003 Nucleic Acids Research  
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

D. L. Wheeler
2006 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  ...  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

D. L. Wheeler
2001 Nucleic Acids Research  
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  
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

D. L. Wheeler
2000 Nucleic Acids Research  
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

D. A. Benson, M. S. Boguski, D. J. Lipman, J. Ostell
1997 Nucleic Acids Research  
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

D. L. Wheeler
2002 Nucleic Acids Research  
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

P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan
2010 Acta Crystallographica Section D: Biological Crystallography  
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]

Assia Rharbi, Khadija Amine, Zohra Bakkoury, Afaf Mikou, Anass Kettani, Abdelkader Betari
2012 Lipoproteins - Role in Health and Diseases  
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

Marco Wiltgen
2009 Current Bioinformatics  
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

Yang Qiu, David H. Maillett, James Knapp, John S. Olson, Austen F. Riggs
2000 Journal of Biological Chemistry  
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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