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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
2012
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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
2021
Fish and Fisheries
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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
2006
Ecology Letters
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.; 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
2013
Genome Biology and Evolution
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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
2010
Nucleic Acids Research
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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
2008
BMC Bioinformatics
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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
2017
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2014
Transactions of the Japanese society for artificial intelligence
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
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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
2013
Nucleic Acids Research
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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
2011
Acta Crystallographica Section D: Biological Crystallography
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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)
2017
Protein Science
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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
2015
Biological Research
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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
2018
Nucleic Acids Research
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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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