A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Filters
UniProt: the universal protein knowledgebase in 2021
2020
Nucleic Acids Research
Preserved Fulltext
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. ...
In this article, we describe significant updates that we have made over the last two years to the resource. ...
ACKNOWLEDGEMENTS The UniProt publication has been prepared by Alex Bateman, Maria ...
doi:10.1093/nar/gkaa1100
pmid:33237286
pmcid:PMC7778908
fatcat:6rwvp6l5uzb3li4lygf2gny6qq
The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms
2021
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Proteoforms are the specific forms of protein molecules expressed by our cells and include the unique combination of post-translational modifications (PTMs), alternative splicing and other sources of variation ...
The HPfA uses a FAIR system to assign persistent identifiers to proteoforms which allows for redundancy calling and tracking from prior and future studies in the growing community of proteoform biology ...
According to UniProt, the total number of 'canonical' (i.e. the representative protein in UniProt for a given gene) human proteins across the entire proteome, is currently 20 386 (2) . ...
doi:10.1093/nar/gkab1086
pmid:34986596
pmcid:PMC8728143
fatcat:72lje2ztvjh4lfzqyq3fjvndje
Online Molecular Initiating Events Prediction Tool Webinar
[article]
2021
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
On Tuesday, 18th May 2021, the NanoCommons team, in a joint initiative with the NanoSafety Cluster, offered an online webinar on the use of their Molecular Initiating Event (MIE) Prediction Tool accessible ...
The existing animal-reliant toxicity testing tools are onerous in terms of time and resources. ...
Frontiers in Plant Science, 2014
Tuesday, May 18, 2021
3
KE, MIE, AO and AOP
Tuesday, May 18, 2021
4
We create databases responsible for three MIEs by creating the MIE gene sets using information ...
doi:10.5281/zenodo.4882651
fatcat:hbys4d7barhk5eart5tttt74hu
Opinion: Standardizing gene product nomenclature—a call to action
2021
Proceedings of the National Academy of Sciences of the United States of America
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Acknowledgments This work was supported in part by grants from the US National ...
The UniProt Knowledgebase (UniProtKB) (12) includes recommended protein names as well as functional, taxonomic, and structural information. ...
In striking contrast to the use of universal identifiers for genes and gene variants, there are no universal identifiers for the peptides and proteins that these genes encode. ...
doi:10.1073/pnas.2025207118
pmid:33408252
fatcat:7miuhc2icneubh4l4c74ybcrcq
Chromosome Walking: A Novel Approach to Analyse Amino Acid Content of Human Proteins Ordered by Gene Position
2021
Applied Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Notwithstanding the huge amount of detailed information available in protein databases, it is not possible to automatically download a list of proteins ordered by the position of their codifying gene. ...
In this study, we developed a new procedure that interrogates two human databases (genomic and protein) and produces a novel dataset of ordered proteins following the mapping of the corresponding genes ...
The most used protein database, UniProt Knowledgebase (Uniprot), gives information on human proteins without ordering based on gene position. ...
doi:10.3390/app11083511
doaj:080dd0f4816346a4babc19d25d967a6b
fatcat:7viqwpo6hvbonddhe7j4ues7lq
Molecular modeling of cornulin (CRNN) for docking with phytocompounds from Justicia adhatoda L
2021
Bioinformation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Thus, we document the optimal binding features of these compounds with the cornulin model for further consideration ...
Therefore, it is of interest to document data on the molecular modeling of cornulin (CRNN) for docking with phytocompounds (Pyrazinamide, Anisotine, Vasicinone, Vasicoline) from Justicia adhatoda L. ...
Materials and Methods: Sequence retrieval and 3D model building: The full amino acid (495aa) sequence of CRNN is downloaded from the Uniprot Knowledgebase database in FASTA format with accession number ...
doi:10.6026/97320630017200
fatcat:7ltfuzkcknbslaqnek74lp5lii
Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer's Disease Mouse Model
2021
Cells
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
To the best of our knowledge, this report is the first to describe PKM1 and STXBP1a overexpression in the OB of an AD mouse model. ...
In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics ...
Cells 2021, 10, 1583 ...
doi:10.3390/cells10071583
pmid:34201730
pmcid:PMC8303486
fatcat:fynmwievcfaa7cbj76nsungcyy
The Gene Ontology resource: enriching a GOld mine
2020
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific ...
As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. ...
ACKNOWLEDGEMENTS We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/ page/acknowledgments-contributors), and all the authors ...
doi:10.1093/nar/gkaa1113
pmid:33290552
pmcid:PMC7779012
fatcat:socxl3x5svamfoc2sobzyvjjoy
CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications
2021
Frontiers in Immunology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future ...
the delta32 variant in complex critical care patients with sepsis. ...
METHODS
Amino Acid Knowledgebase and Human Genomic Variants The human CCR5 protein sequence (UniProt P51681) was assessed on NCBI BLAST (53) against the Homo sapiens UniProtKB/Swiss-Prot database, ...
doi:10.3389/fimmu.2021.790041
pmid:34925370
pmcid:PMC8674737
fatcat:iedtuq7buzf5fjipawbc7todmu
14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations
[article]
2021
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations ...
An additional outcome of this work is a set of publications for UniProt entries with annotations that can be submitted to the UniProt Knowledgebase via the community submission system. ...
15th
Category: Curation and Data Visualization Tools; Functional Annotation The UniProt Knowledgebase (UniProtKB, https://www.uniprot.org) is a comprehensive, high quality and freely accessible resource ...
doi:10.5281/zenodo.5570276
fatcat:nlbkkzkhfvhdddqu4ypzh247iy
Structure-Based Virtual Screening of Essential Mycobacterium Tuberculosis Enzymes AspS and KatG for potential inhibitors
2021
Bioinformation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
We used the Protein Databank (PDB), the UniProt Knowledgebase and the iDock server in this study. ...
The intermolecular forces responsible for the differing binding affinities of each enzyme are primarily Coulombic interactions for AspS, versus Coulombic and extensive hydrogen bonding interactions in ...
This process narrowed the list of possible enzymes to target to only two: KatG and AspS. To sequence the enzyme, the UniProt Knowledgebase was utilized. ...
doi:10.6026/97320630017101
fatcat:bpxyd5wn4bhijerq263gfrckue
Binding site identification of COVID-19 main protease 3D structure by homology modeling
2021
Indonesian Journal of Electrical Engineering and Computer Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
DeepSite algorithm elucidates the binding site area that captured local patterns in the structure and exposed the surface cavity of the binding pocket of this protein. ...
The main result of this study suggests that blocking expression of the protein may constitute an efficient approach for transmission blockage. ...
ACKNOWLEDGEMENTS The first author would like to appreciate the postgraduate research directorate of Durban University of Technology in South Africa for the postdoctoral fellowship award to conduct this ...
doi:10.11591/ijeecs.v21.i3.pp1713-1721
fatcat:dyxlkig26zbxfh266jotocfiae
Rigorous estimation of post-translational proteasomal splicing in the immunopeptidome
[article]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Here, we describe a peptide source assignment workflow to rigorously assign the source of de novo sequenced peptides and find that the estimated extent of post-translational splicing in the immunopeptidome ...
We believe our approach furthers the understanding of post-translationally spliced peptides and thus improves the characterization of immunopeptidome which plays a critical role in the immune response ...
UniProt: The universal protein knowledgebase. Nucleic Acids Res. (2017)
373
doi:10.1093/nar/gkw1099.
374
31. Ma, B. & Johnson, R. De novo sequencing and homology searching. ...
doi:10.1101/2021.05.26.445792
fatcat:hagsrtcvpjg2jk4wtplkwd4ocu
Label-Free Quantitative Proteomic Analysis of Harmless and Pathogenic Strains of Infectious Microalgae, Prototheca spp
2016
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
protothecoides resulted in the identification of 226 proteins. ...
Therefore, in the present study we investigated the protein expression level difference between the genotypes of P. zopfii and P. blaschkeae. ...
We would like to acknowledge the assistance of the Bio-MS unit of the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). ...
doi:10.3390/ijms18010059
pmid:28036087
pmcid:PMC5297694
fatcat:ydnwy5jfq5e6zek4zdflwp2liu
In Silico Study to Predict the Structural and Functional Consequences of SNPs on Biomarkers of Ovarian Cancer (OC) and BPA Exposure-Associated OC
2022
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Future in vitro studies should provide further insight into the role of this transporter protein in UCEC. ...
Conclusions: We demonstrate that the R831C/R804C mutation is deleterious and the predicted ΔΔG values suggest that the mutation reduces the stability of the protein. ...
Acknowledgments: We would like to thank Carlos Outeiral, Oxford Protein Informatics Group, University of Oxford, for his useful discussions on the manuscript. ...
doi:10.3390/ijms23031725
pmid:35163645
pmcid:PMC8835975
fatcat:ke5lqx452bbonea7cl6ib35ktq
« Previous
Showing results 1 — 15 out of 285 results