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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

Sameer Velankar, José M. Dana, Julius Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria-Jesus Martin, Gerard J. Kleywegt
2012 Nucleic Acids Research  
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/ sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt.  ...  The SIFTS process includes crossreferences to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database.  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as well as the structural bioinformatics community for using SIFTS data and providing  ... 
doi:10.1093/nar/gks1258 pmid:23203869 pmcid:PMC3531078 fatcat:rnyow6huf5grfp5fz4oyien7zm

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

Jose M Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Martin, Sameer Velankar
2018 Nucleic Acids Research  
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts/) was established in 2002 and continues to operate as a collaboration between the Protein Data Bank  ...  The resource is instrumental in the transfer of annotations between protein structure and protein sequence resources through provision of up-to-date residue-level mappings between entries from the PDB  ...  We also like to thank all partners at EMBL and EMBL-EBI, wwPDB and in the wider structural bioinformatics community for using SIFTS and for providing valuable feedback on its development.  ... 
doi:10.1093/nar/gky1114 pmid:30445541 pmcid:PMC6324003 fatcat:uiz3iloopze3blz2pxjfesfthm

Sifting environmental DNA metabarcoding data sets for rapid reconstruction of marine food webs

Simone D'Alessandro, Stefano Mariani
2021 Fish and Fisheries  
It is, therefore, essential to devise and implement methods that can rapidly and inexpensively monitor changes in the marine food web structure.  ...  Although the trophic webs obtained are a simplified approximation of those constructed with traditional methods, they generate realistic networks that fit with expectations, and allow ecological inference  ...  These data can be used to explore the trophic structure of marine communities inhabiting certain areas and may lead to useful, integrated information for management interventions.  ... 
doi:10.1111/faf.12553 fatcat:3i3ccdiqlbf33lvjedyjw3nbkq

Patterns in body mass distributions: sifting among alternative hypotheses

C. R. Allen, A. S. Garmestani, T. D. Havlicek, P. A. Marquet, G. D. Peterson, C. Restrepo, C. A. Stow, B. E. Weeks
2006 Ecology Letters  
.; and Weeks, B. E., "Patterns in body mass distributions: sifting among alternative hypotheses" (2006). Papers in Natural Resources. 105.  ...  Energetic and textural discontinuity hypotheses focus upon the allometry of resource use.  ...  Body mass is the most ecologically integrative attribute of a species, and may be a Ôtaxon-freeÕ attribute (Damuth 1992) , thus recognizing patterns in body mass structure can provide clues about the  ... 
doi:10.1111/j.1461-0248.2006.00902.x pmid:16643307 fatcat:npyg7qqypvdnrfyl27k55gln34

Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont

Timothy Driscoll, Joseph J. Gillespie, Eric K. Nordberg, Abdu F. Azad, Bruno W. Sobral
2013 Genome Biology and Evolution  
These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA.  ...  This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions.  ...  B.W.S. and R01AI017828 and R01AI59118 to A.F.A.  ... 
doi:10.1093/gbe/evt036 pmid:23475938 pmcid:PMC3641634 fatcat:qk3j6xil6jdnleidtoysffnihq

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  
SIFTS is widely used by major bioinformatics resources.  ...  PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information.  ...  depositing their structures and experimental data in the PDB and EMDB.  ... 
doi:10.1093/nar/gkq985 pmid:21045060 pmcid:PMC3013808 fatcat:732ckrjoq5afnk3jt2i7jwjcvy

SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase

Fabrice PA David, Yum L Yip
2008 BMC Bioinformatics  
Sequences and structures provide valuable complementary information on protein features and functions.  ...  SSMap is the first isoform sequence-specific mapping resource and is up-to-date for UniProtKB annotation tasks.  ...  Acknowledgements The authors wish to thank Anne-Lise Veuthey, Ursula Hinz and Amos Bairoch for constructive feedback on the manuscript.  ... 
doi:10.1186/1471-2105-9-391 pmid:18811932 pmcid:PMC2567350 fatcat:arztkik62rffndmxexwz3xa6j4

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.  ...  The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and  ...  ACKNOWLEDGEMENTS We would like to thank all collaborators and partners at the EMBL-EBI, EMBL, wwPDB, EMDB, CCP4, SASBDB, CCPN, CCDC, CEITEC, MRC-LMB and other collaborative efforts, as well as the structural  ... 
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
2009 Nucleic Acids Research  
PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis  ...  PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as  ... 
doi:10.1093/nar/gkp916 pmid:19858099 pmcid:PMC2808887 fatcat:amgz3equ6jgenhym77vbghy47e

Linked Open Data Construction of Purpose Oriented Interactomics by Integration of Life Sciences LOD
生命科学の複数LODの統合による目的別タンパク質分子間相互作用Linked Open Dataの構築

Yusuke Komiyama, Masaki Banno, Masayuki Yarimizu, Fumihiro Kato, Ikki Ohmukai, Hideak Takeda, Kentaro Shimizu
2014 Transactions of the Japanese society for artificial intelligence  
Especially RDF-SIFTS (Structure Integration with Function, Taxonomy and Sequence) that is an aggregate of 10 small LOD was constructed in the short period of BioHackathon 2013 or was developed in one week  ...  It could be combined with public LOD of the life science domain of 28,529,064,366 triples and was able to be searched.  ...  cc2type . } LIMIT 100 4·3 LOD EBI (European Bioinformatics Institute) SIFTS (Structure integration with function, taxonomy and sequence) [Ve- lankar 13] RDF LOD .  ... 
doi:10.1527/tjsai.29.356 fatcat:lzp5oohlsrakzjnkl4jopp2qby

PDBe: Protein Data Bank in Europe

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley (+15 others)
2013 Nucleic Acids Research  
Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis  ...  of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.  ...  They are also particularly indebted to the structural biology community for depositing the fruit of their work in the PDB, BMRB and EMDB archives. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Sameer Velankar, Gerard J. Kleywegt
2011 Acta Crystallographica Section D: Biological Crystallography  
This collaboration, which started in 2000, has resulted in a data resource called SIFTS (Structure Integration with Function, Taxonomy and Sequences; Velankar et al., 2005) .  ...  PDBe collaborates primarily with UniProt (UniProt Consortium, 2009) to integrate information from protein sequences and structures.  ... 
doi:10.1107/s090744491004117x pmid:21460450 pmcid:PMC3069747 fatcat:gpse5hxwwvbyxbqhrrsodahkye

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
2017 Protein Science  
the integration of PDBj and BMRB searches.  ...  In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated  ...  In order to integrate the PDB data with other biological information, it includes the resource of SIFTS (Structure integration with function, taxonomy, and sequence), 8 which has been developed by EMBL-EBI  ... 
doi:10.1002/pro.3273 pmid:28815765 pmcid:PMC5734392 fatcat:7ttn55ucxvcjfjkmivznvmet34

CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

Shabana Kouser Ali, C George Priya Doss, D Thirumal Kumar, Hailong Zhu
2015 Biological Research  
We hope our database will act as a useful reference resource for hematologists to reveal protein structure-function relationship and disease genotype-phenotype correlation.  ...  This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information.  ...  Compliance with ethical guidelines Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s40659-015-0028-5 pmid:26187044 pmcid:PMC4506595 fatcat:xnjzsytipzbc3f3mlwl4uj26hu

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
2018 Nucleic Acids Research  
Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals  ...  and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around  ...  We gratefully acknowledge contributions from past members of the RCSB PDB team and our Worldwide Protein Data Bank partners.  ... 
doi:10.1093/nar/gky1004 pmid:30357411 pmcid:PMC6324064 fatcat:clctmqo6ujaifm7s27vk3s2h7i
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