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Protein structure databases with new web services for structural biology and biomedical research

D. M. Standley, A. R. Kinjo, K. Kinoshita, H. Nakamura
2008 Briefings in Bioinformatics  
Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation  ...  and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe.  ...  PDBj is financially supported by the Japan Science and Technology Agency, Institute for Bioinformatics Research and Development (JST-BIRD).  ... 
doi:10.1093/bib/bbn015 pmid:18430752 fatcat:rmlvhckicrcn7m4b2yvzniiaq4

The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database

J. S. Garavelli
2001 Nucleic Acids Research  
The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank.  ...  citations with database crossreferences, structural diagrams and molecular models.  ...  The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank (7) .  ... 
doi:10.1093/nar/29.1.199 pmid:11125090 pmcid:PMC29832 fatcat:j7ma7jp6ive6rcsryryz3svb3m

PubChem BioAssay: 2014 update

Yanli Wang, Tugba Suzek, Jian Zhang, Jiyao Wang, Siqian He, Tiejun Cheng, Benjamin A. Shoemaker, Asta Gindulyte, Stephen H. Bryant
2013 Nucleic Acids Research  
chemistry studies, chemical biology research and drug discovery programs.  ...  to streamline chemical structure and bioassay submissions.  ...  ACKNOWLEDGEMENTS The authors thank all submitters who have contributed data to PubChem and the rest of the PubChem team for their support.  ... 
doi:10.1093/nar/gkt978 pmid:24198245 pmcid:PMC3965008 fatcat:57wu2puoovaevlpqtrp5pjsq7e

Bioinformatics: Basics, Development, and Future [chapter]

Ibrokhim Y. Abdurakhmonov
2016 Bioinformatics - Updated Features and Applications  
and design; building biological networks; development of databases and data management systems; development of software and analysis tools; bioinformatics services and workflow; mining of biomedical literature  ...  Bioinformatics research and application include the analysis of molecular sequence and genomics data; genome annotation, gene/protein prediction, and expression profiling; molecular folding, modeling,  ...  for structural biology and medicinal drug design [12, 13] .  ... 
doi:10.5772/63817 fatcat:otwfgrcmgfdglibb5afk2oktce

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

Margaret J. Gabanyi, Paul D. Adams, Konstantin Arnold, Lorenza Bordoli, Lester G. Carter, Judith Flippen-Andersen, Lida Gifford, Juergen Haas, Andrei Kouranov, William A. McLaughlin, David I. Micallef, Wladek Minor (+6 others)
2011 Journal of Structural and Functional Genomics  
Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events  ...  The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: is an open web resource designed to turn the products of the structural genomics and structural biology  ...  Acknowledgments The SBKB is a resource center within the Protein Structure Initiative and is supported by grant U01 GM093324-01 from the National Institute of General Medical Sciences.  ... 
doi:10.1007/s10969-011-9106-2 pmid:21472436 pmcid:PMC3123456 fatcat:335qzn5h3relxbq4n7lomjdcpa

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
2016 Journal of Biomedical Semantics  
proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes.  ...  However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases.  ...  Owing to the machine readability of the XML format, the BMRB/XML provides users with an excellent starting point to develop new tools for use in biochemistry and structural biology.  ... 
doi:10.1186/s13326-016-0057-1 pmid:27927232 pmcid:PMC5143449 fatcat:kidpbvthwbgzjko7jvgesbepqm

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek (+12 others)
2014 Nucleic Acids Research  
It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on, SIB's Bioinformatics Resource Portal  ...  This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.  ...  Structural bioinformatics and drug design SWISS-MODEL ( is a fully automated web-based protein structure homologymodeling expert system.  ... 
doi:10.1093/nar/gku380 pmid:24792157 pmcid:PMC4086091 fatcat:ps6txa3xijhpxbpl2radc6dvdi

Natural Language Processing and Unsupervised Learning: It's Significance on Biomedical Literature

Kanika Gupta, Ashok Kumar
2018 International Journal of Current Research and Review  
arising in the biomedical research and would also help in the development of new hypothesis.  ...  It is therefore not possible for researchers and practitioners to automatically extract and relate information from different written resources.  ...  The authors are also grateful to authors / editors / publishers of all those articles, journals and books from where the literature for this article has been reviewed and discussed.  ... 
doi:10.31782/ijcrr.2018.10143 fatcat:n56phwi4mfa4jkwgutik5r64ze

The Protein Model Portal

Konstantin Arnold, Florian Kiefer, Jürgen Kopp, James N. D. Battey, Michael Podvinec, John D. Westbrook, Helen M. Berman, Lorenza Bordoli, Torsten Schwede
2008 Journal of Structural and Functional Genomics  
research center for structural genomics PDB Protein Data Bank PMP Protein Model Portal PSI SGKB PSI structural genomics knowledgebase PSI Protein structure initiative SIB  ...  proteins JCMM Joint center for molecular modeling JCSG Joint center for structural genomics MCSG Midwest center for structural genomics NESG Northeast structural genomics consortium NYSGXRC New York SGX  ...  the original author(s) and source are credited.  ... 
doi:10.1007/s10969-008-9048-5 pmid:19037750 pmcid:PMC2704613 fatcat:nq7bh44pt5eg3fzq7ij5dze6xq

BioMetaDB: Ontology-based Classification and Extension of Biodatabases

Ching-Fen Chang, Chang-Hsien Lin, Chuan-Hsiung Chang
2014 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms  
The types of databases included DNA database, RNA database, protein database, structure database, microarray database, etc.  ...  from public databases; (2) creating an integrated ontology repository for biological and medical studies based on expert-tagged corpus; (3) establish web services to enable users to access all their desired  ...  Web Services To implement useful web services of BioMetaDB that are accessed through internet connection, we had set up a web server.  ... 
doi:10.5220/0004801001560163 dblp:conf/biostec/ChangLC14 fatcat:h5drlsgthfhcnfylmmrzw6tlem

geWorkbench: an open source platform for integrative genomics

Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano
2010 Computer applications in the biosciences : CABIOS  
domains (gene expression, sequence, protein structure and systems biology).  ...  data, annotation and computational servers, thus, enabling researchers with limited local resources to benefit from available public infrastructure.  ...  ACKNOWLEDGEMENTS We thank the many people who have made significant contributions to geWorkbench, from past and present members of the core development team (Kiran Keshav, Min You, Thomas Garben, Oleg  ... 
doi:10.1093/bioinformatics/btq282 pmid:20511363 pmcid:PMC2894520 fatcat:wgswns6buracjplgmtgxligczq

A library-based bioinformatics services program

S Yarfitz, D S Ketchell
2000 Bulletin of the Medical Library Association  
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries.  ...  Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site.  ...  ACKNOWLEDGMENTS The authors thank Catherine Burroughs for assistance with the Bioinformatics Series evaluation survey and helpful comments on the manuscript, and Doug Schaad for help with the analysis  ... 
pmid:10658962 pmcid:PMC35196 fatcat:pmauxzs5czcevemqhwibjk7jpe

Multiple database coverage of structural biology

Claudia Lascar, Loren D Mendelsohn
2002 Journal of the Medical Library Association  
In this way, relevant articles on structural biology can be quickly identified and obtained for researchers through document delivery services.  ...  Medical librarians play a decisive role in supporting such biomedical research by developing strong print and electronic collections in structural biology and by instructing researchers on how to search  ... 
pmid:11999187 pmcid:PMC100774 fatcat:ywsgfpeoxvahhasrqfoae2q6cm

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, A. Alili, C. Best, H. C. Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas (+21 others)
2010 Nucleic Acids Research  
PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community.  ...  The SIFTS initiative is an example of such a collaboration-it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases.  ...  ACKNOWLEDGEMENTS The authors wish to thank all collaborators and partners in the EBI, EMBL, wwPDB, EMDB, CCPN, CCP4, CCDC and other collaborative efforts, as well as the structural biology community for  ... 
doi:10.1093/nar/gkq985 pmid:21045060 pmcid:PMC3013808 fatcat:732ckrjoq5afnk3jt2i7jwjcvy

Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh

Ansuman Chattopadhyay, Nancy Hrinya Tannery, Deborah A L Silverman, Phillip Bergen, Barbara A Epstein
2006 Journal of the Medical Library Association  
In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing  ...  The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages.  ...  protein, and structure databases.  ... 
pmid:16888665 pmcid:PMC1525320 fatcat:ubsfdp4eanhbnhazfkd47oblae
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