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PDBe-KB: a community-driven resource for structural and functional annotations

Mihaly Varadi, PDBe-KB Consortium
2021 Acta Crystallographica Section A: Foundations and Advances  
functional annotations of molecular structure data [1].  ...  The Protein Data Bank in Europe -Knowledge Base (PDBe-KB, is a community-driven, collaborative data resource that provides literature-derived, curated and predicted structural and  ...  We have also created web pages called "Aggregated Views" that provide an overview of all the structure data related to a full-length protein (i.e. UniProtKB accession).  ... 
doi:10.1107/s0108767321090024 fatcat:j3onl6osbzbgbawaid5m7ggftu

PDBe-KB: a community-driven resource for structural and functional annotations

2019 Nucleic Acids Research  
We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries.  ...  The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable  ...  ACKNOWLEDGEMENTS We would like to thank all the members of PDBe team for their continued support of the design and development of PDBe-KB.  ... 
doi:10.1093/nar/gkz853 pmid:31584092 pmcid:PMC6943075 fatcat:lbpb4ss3ynaetnusqksvrbjy6y

Openaire2020 D7.5 – Data Citation Standards And Index Requirements

Florian Graef, Jo McEntyre
2016 Zenodo  
This deliverable report gives an overview of data citation practices across earth-, life-, social sciences and humanities.  ...  It furthermore introduces a tool developed to ease standard compliant data citation and discusses data citation indexes and metrics.  ...  With the emergence of research methods that have a high data output, as well as an increasing number of open access policies in place, the graph is expected to grow.  ... 
doi:10.5281/zenodo.1257268 fatcat:yov25ukfxze63ml3t2s47vyici

Databases and Archiving for CryoEM [chapter]

A. Patwardhan, C.L. Lawson
2016 Methods in Enzymology  
These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed and integrated with other structural  ...  The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication.  ...  Acknowledgments We thank the many current and past colleagues who have made significant contributions to the development of data archiving for 3DEM methods.  ... 
doi:10.1016/bs.mie.2016.04.015 pmid:27572735 pmcid:PMC5351295 fatcat:kwqh4wmdhzb5rily4f6i2y53x4

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng (+26 others)
2020 Nucleic Acids Research  
, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of users around  ...  data integrated with >40 external biodata resources.  ...  We thank the 40 000+ PDB data depositors who have contributed to the growth of the PDB archive since 1971 and gratefully acknowledge contributions from past members of the RCSB PDB team and our Worldwide  ... 
doi:10.1093/nar/gkaa1038 pmid:33211854 pmcid:PMC7779003 fatcat:dkqo54quqjgovp7y4v67b635zu

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
data have enabled us to make these data available to external developers through the new PDBe API (see Molecular structure and PDBe development).  ...  PDBe Content and Integration The aim of PDBe is to serve the biomedical community by providing easy access to macromolecular and cellular structure data.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

BioExcel Deliverable 2.6 – Integration of BioExcel software framework with standards and international initiatives

Stian Soiland-Reyes, Adam Hospital, Genís Bayarri, Ania Niewelska, Cibin Sadasivan Baby, Douglas Lowe, Pau Andrio, Josep Ll. Gelpi
2022 Zenodo  
An ongoing challenge for users to take advantage of BioExcel tools in workflow management systems and across multiple compute infrastructures is to get the software installed and integrated into their  ...  Our work on forming the BioExcel Building Blocks (BioBB) have helped unify programmatic invocation of biomolecular simulation and modelling tools, making it easier to include them in major workflow systems  ...  The markup is embedded within the HTML of the resource pages (Figure 1 ), from where it can be programmatically extracted and integrated into a knowledge graph.  ... 
doi:10.5281/zenodo.5824544 fatcat:kgwzhob3cbayfdp4tgxcqzutwu

PDBe-KB: collaboratively defining the biological context of structural data

PDBe-KB consortium
The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner  ...  The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations  ...  ACKNOWLEDGEMENTS We thank all the members of the PDBe team for their continued support of the design and development of PDBe-KB.  ... 
doi:10.1093/nar/gkab988 pmid:34755867 pmcid:PMC8728252 fatcat:fsl366s2jfdobge6gvqctu4zva

Heterogeneous Data Processing for Information and Knowledge Management in Glycomics and Glycoproteomics

Julien Mariethoz, Frédérique Lisacek
During the multiple projects related to this thesis, I was also privileged to collaborate and learn from many individuals and groups. There are too many people to name them all.  ...  Finally, special thanks to my family, especially Carole, Hugo, and Alexandre, for their infinite patience and unconditional support. iv  ...  . ¶ ¶ To whom correspondence should be addressed: SIB Swiss Institute of Bioinformatics, Proteome Informatics Group, Route de Drize 7, 1227 Geneva, Switzerland.  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4

Orders of disorder: computational analysis of the interactions of intrinsically disordered proteins

Erzsébet Fichó, Bálint Mészáros
. ▪ Mészáros B, Dobson L, Fichó E, Tusnády EG, Dosztányi Z, Simon I: How folding and binding intertwine during protein complex formation provides an additional layer of functional regulation.  ...  under the guidance of Prof. István Simon and the supervision of Dr. Bálint Mészáros.  ...  access to the data they contain.  ... 
doi:10.15476/elte.2018.256 fatcat:dexyhyzkybedtmu25t4ub2ig2a

Bioinformatics analysis of proteins and proteomes

Islam Mohammad
The advancement of next-generation proteomics methodologies has led to an explosion in proteomics data.  ...  ProtAnnotator 2.0 automated the process and provides an update to the annotation of the truffle proteome.  ...  Acknowledgements I am indebted to many individuals throughout my Ph.D. tenure for their assistance and support. The format of this thesis will not permit me to list every one of them.  ... 
doi:10.25949/19433357 fatcat:idrznpnkmfctfoxypc5cztsn3m