Westhof E, Leontis N B
An RNA-centric historical narrative around the Protein Data Bank Article de journal
Dans: J Biol Chem, vol. 296, p. 100555, 2021, ISBN: 33744291, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF
@article{Westhof2021,
title = {An RNA-centric historical narrative around the Protein Data Bank},
author = {E Westhof and N B Leontis},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33744291},
doi = {10.1016/j.jbc.2021.100555},
isbn = {33744291},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Biol Chem},
volume = {296},
pages = {100555},
abstract = {Some of the amazing contributions brought to the scientific community by the PDB are described. The focus is on nucleic acid structures with a bias towards RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article
Review},
keywords = {Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Thompson J D, Holbrook S R, Katoh K, Koehl P, Moras D, Westhof E, Poch O
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences Article de journal
Dans: Nucleic Acids Res, vol. 33, no. 13, p. 4164-4171, 2005, ISBN: 16043635, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Controlled, Databases, DNA/*methods Sequence Analysis, Genetic Humans Interleukin-1/genetics Internet Research Support, Non-U.S. Gov't Sequence Alignment/*methods Sequence Analysis, Protein/*methods Sequence Analysis, RNA/*methods *Software Systems Integration Vocabulary, Unité ARN, WESTHOF
@article{,
title = {MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences},
author = {J D Thompson and S R Holbrook and K Katoh and P Koehl and D Moras and E Westhof and O Poch},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16043635},
isbn = {16043635},
year = {2005},
date = {2005-01-01},
journal = {Nucleic Acids Res},
volume = {33},
number = {13},
pages = {4164-4171},
abstract = {The application of high-throughput techniques such as genomics, proteomics or transcriptomics means that vast amounts of heterogeneous data are now available in the public databases. Bioinformatics is responding to the challenge with new integrated management systems for data collection, validation and analysis. Multiple alignments of genomic and protein sequences provide an ideal environment for the integration of this mass of information. In the context of the sequence family, structural and functional data can be evaluated and propagated from known to unknown sequences. However, effective integration is being hindered by syntactic and semantic differences between the different data resources and the alignment techniques employed. One solution to this problem is the development of an ontology that systematically defines the terms used in a specific domain. Ontologies are used to share data from different resources, to automatically analyse information and to represent domain knowledge for non-experts. Here, we present MAO, a new ontology for multiple alignments of nucleic and protein sequences. MAO is designed to improve interoperation and data sharing between different alignment protocols for the construction of a high quality, reliable multiple alignment in order to facilitate knowledge extraction and the presentation of the most pertinent information to the biologist.},
note = {1362-4962
Journal Article},
keywords = {Controlled, Databases, DNA/*methods Sequence Analysis, Genetic Humans Interleukin-1/genetics Internet Research Support, Non-U.S. Gov't Sequence Alignment/*methods Sequence Analysis, Protein/*methods Sequence Analysis, RNA/*methods *Software Systems Integration Vocabulary, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}