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UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
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

Michael A R Hollas, Matthew T Robey, Ryan T Fellers, Richard D LeDuc, Paul M Thomas, Neil L Kelleher
2021 Nucleic Acids Research  
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]

Abhijit Dasgupta, Vadim Zhernovkov, Boris Kholodenko, Vladimir Lobaskin, Martin Himly
2021 Zenodo  
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

Kenji Fujiyoshi, Elspeth A. Bruford, Pawel Mroz, Cynthe L. Sims, Timothy J. O'Leary, Anthony W. I. Lo, Neng Chen, Nimesh R. Patel, Keyur Pravinchandra Patel, Barbara Seliger, Mingyang Song, Federico A. Monzon (+7 others)
2021 Proceedings of the National Academy of Sciences of the United States of America  
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

Annamaria Vernone, Chiara Ricca, Gianpiero Pescarmona, Francesca Silvagno
2021 Applied Sciences  
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

Jayaraman Selvaraj, Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
2021 Bioinformation  
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

Esdras Matheus Gomes da Silva, Letícia Graziela Costa Santos, Flávia Santiago de Oliveira, Flávia Cristina de Paula Freitas, Vinícius da Silva Coutinho Parreira, Hellen Geremias dos Santos, Raphael Tavares, Paulo Costa Carvalho, Ana Gisele da Costa Neves-Ferreira, Andrea Siqueira Haibara, Patrícia Savio de Araujo-Souza, Adriana Abalen Martins Dias (+1 others)
2021 Cells  
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

Gene Ontology Consortium
2020 Nucleic Acids Research  
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 ( 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

Jacob Bauss, Michele Morris, Rama Shankar, Rosemary Olivero, Leah N. Buck, Cynthia L. Stenger, David Hinds, Joshua Mills, Alexandra Eby, Joseph W. Zagorski, Caitlin Smith, Sara Cline (+7 others)
2021 Frontiers in Immunology  
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]

Federica Quaglia
2021 Zenodo  
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, 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

Andrew P. Collins, University of Central Florida College of Medicine, Orlando, Florida, 2University of Washington, Seattle, WA
2021 Bioinformation  
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

Marion Adebiyi, Oludayo O. Olugbara
2021 Indonesian Journal of Electrical Engineering and Computer Science  
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]

Kamil J Cygan, Ehdieh Khaledian, Lili Blumenberg, Robert R Salzler, Darshit Shah, William Olson, Lynn E Macdonald, Andrew J Murphy, Ankur Dhanik
2021 bioRxiv   pre-print
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

Jayaseelan Murugaiyan, Murat Eravci, Christoph Weise, Uwe Roesler
2016 International Journal of Molecular Sciences  
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

Aeman Zahra, Marcia Hall, Jayanta Chatterjee, Cristina Sisu, Emmanouil Karteris
2022 International Journal of Molecular Sciences  
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
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