SIB - Swiss Institute of Bioinformatics
SIB - Swiss Institute of Bioinformatics
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Enzymes: Extracting Biological Insight Using UniProt
UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information. Enhanced enzyme annotation in UniProtKB is based on Rhea, a comprehensive expert-curated database of biochemical reactions that uses the ChEBI ontology to describe reaction participants.
Starting with a biological question (I.e., Could you refine my list of enzymes to identify the ones with cysteine at the active and/or allosteric sites?), you will explore the different ways of answering it, using UniProt's advanced query, or SPARQL when the use of UniProt advanced queries is not applicable. Hints on how to extend queries to other biological contexts will also be provided.
This webinar introduces the enzyme-related data in UniProt and how to find it. The video was recorded live during the SIB course streamed on June 6, 2024.
Target audience: This webinar is for beginners interested in protein enzymes.
Speakers: Elisabeth Gasteiger and Jerven Bolleman, Swiss-Prot group
Any question about this talk? Contact UniProt at www.uniprot.org/contact
Links:
UniProt: www.uniprot.org/
Rhea: www.rhea-db.org/
ChEBI: www.ebi.ac.uk/chebi/
SPARQL: sparql.uniprot.org/
Swiss-Prot group: www.sib.swiss/swiss-prot
Chapters:
0:00 - Introduction
0:27 - Part I: What you need to know to make your UniProtKB queries meaningful
31:46 - Part II: SPARQL
zhlédnutí: 229

Video

Detecting inbreeding depression in structured populations
zhlédnutí 174Před 2 měsíci
What you will discover: a mixed model with an allele-sharing-based relatedness matrix to estimate more efficiently inbreeding depression in structured populations. You are: a biologist or bioinformatician who needs to estimate the inbreeding depression in a group of related individuals Speaker: Eléonore Lavanchy, a member in Jérôme Goudet’s group based in Unil in Lausanne. Click to access speci...
GeneSelectR: how to identify relevant features in RNA sequencing datasets
zhlédnutí 308Před 3 měsíci
What you will discover: GeneSelectR, an open-source R package that innovatively combines ML and bioinformatic data mining approaches for enhanced feature selection during High-dimensional Bulk RNA sequencing. You are: a bioinformatician who performs bulk RNAseq analysis but struggles with batch effects Speaker: Damir Zhakparov, a PhD candidate in Katja Baerenfaller’s group based in Swiss Instit...
Wilhelm Dirks - Cell lines in the 21st century symposium
zhlédnutí 81Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Tadashi Kondo - Cell lines in the 21st century symposium
zhlédnutí 33Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Niels C. Bols - Cell lines in the 21st century symposium
zhlédnutí 45Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Jan van der Valk - Cell lines in the 21st century symposium
zhlédnutí 40Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Florian M. Wurm - Cell lines in the 21st century symposium
zhlédnutí 56Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Anita Bandrowski - Cell lines in the 21st century symposium
zhlédnutí 31Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Amos Bairoch - Cell lines in the 21st century symposium
zhlédnutí 38Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Andreas Kurtz - Cell lines in the 21st century symposium
zhlédnutí 44Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
Amanda Capes Davis - Cell lines in the 21st century symposium
zhlédnutí 80Před 4 měsíci
In January 2024, the Cellosaurus team organized a symposium on “Cell lines in the 21st century”. The symposium aimed to tackle the critical issue of cell line misidentification and promote best practices in cell line management. Discover presentations from international experts: Jamie Almeida, NIST, USA: "Standards needed in mouse cell line authentication" Amos Bairoch, SIB, Switzerland: "Cello...
CellCharter: flexible and scalable spatial cell niches
zhlédnutí 157Před 4 měsíci
What you will discover: CellCharter is a computational framework designed to uncover and analyze communities of cells within tissues. Its primary goal is to reveal how distinct types of cell band together and function in targeted areas. In this video, you will also see how you can use CellCharter to detect artifacts from immunofluorescence data. You are: a cancer biologist, developmental biolog...
An Introduction to Nextflow and nf-core
zhlédnutí 397Před 5 měsíci
This talk was recorded live during the SIB course “ Reproducible Research and Data Analysis using Nextflow Pipelines” (www.sib.swiss/training/course/20211115_NEXTF) which took place online on 15-18 November 2021. The course material can be found on the dedicated course GitHub repository (github.com/biocorecrg/SIB_course_nextflow_Nov_2021?tab=readme-ov-file) and course GitHub Page (biocorecrg.gi...
Easy simulation of species trees and populations over time using ReMASTER
zhlédnutí 84Před 5 měsíci
What you will discover: ReMASTER, a phylodynamic simulation tool designed for BEAST 2 to analyze molecular sequences. You are: an evolutionary biologist, epidemiologist - or generally interested in phylodynamic simulations, then this talk is for you! Speaker: Tim Vaughan, Senior Scientist at Computational Evolution led by Tanja Stadler. Click to access specific sections of the talk: - 00:53 Lea...
How to boost your research with SIB’s Semantic Web of data
zhlédnutí 257Před 5 měsíci
How to boost your research with SIB’s Semantic Web of data
prolfqua: A comprehensive R package for protein differential expression analysis
zhlédnutí 865Před 8 měsíci
prolfqua: A comprehensive R package for protein differential expression analysis
Reading tabulated data with pandas (1 of 9)
zhlédnutí 153Před 9 měsíci
Reading tabulated data with pandas (1 of 9)
Data manipulation: selecting rows and columns (2 of 9)
zhlédnutí 79Před 9 měsíci
Data manipulation: selecting rows and columns (2 of 9)
Data Analysis and Representation in Python - DataFrame subsetting (3 of 9)
zhlédnutí 58Před 9 měsíci
Data Analysis and Representation in Python - DataFrame subsetting (3 of 9)
Data Analysis and Representation in Python - Operations on columns (4 of 9)
zhlédnutí 39Před 9 měsíci
Data Analysis and Representation in Python - Operations on columns (4 of 9)
Data Analysis and Representation in Python - Deleting and adding rows, and writing to file (5 of 9)
zhlédnutí 39Před 9 měsíci
Data Analysis and Representation in Python - Deleting and adding rows, and writing to file (5 of 9)
Data Analysis and Representation in Python - Basic description, common summary statistics (6 of 9)
zhlédnutí 90Před 9 měsíci
Data Analysis and Representation in Python - Basic description, common summary statistics (6 of 9)
Data Analysis and Representation in Python - Basic representation: plotting one column (7 of 9)
zhlédnutí 44Před 9 měsíci
Data Analysis and Representation in Python - Basic representation: plotting one column (7 of 9)
Data Analysis and Representation in Python - Accounting for categories in the data (8 of 9)
zhlédnutí 53Před 9 měsíci
Data Analysis and Representation in Python - Accounting for categories in the data (8 of 9)
Data Analysis and Representation in Python - scatter/line plots, exporting, and conclusion (9 of 9)
zhlédnutí 57Před 9 měsíci
Data Analysis and Representation in Python - scatter/line plots, exporting, and conclusion (9 of 9)
Using ASAP for Single-Cell Analysis
zhlédnutí 511Před 9 měsíci
Using ASAP for Single-Cell Analysis
Optimizing Python Code for Better Performance - Timing objects in python (1 of 8)
zhlédnutí 224Před 9 měsíci
Optimizing Python Code for Better Performance - Timing objects in python (1 of 8)
Optimizing Python Code for Better Performance - Time profiling in python (2 of 8)
zhlédnutí 105Před 9 měsíci
Optimizing Python Code for Better Performance - Time profiling in python (2 of 8)
Optimizing Python Code for Better Performance - Measuring RAM usage in python (3 of 8)
zhlédnutí 98Před 9 měsíci
Optimizing Python Code for Better Performance - Measuring RAM usage in python (3 of 8)

Komentáře

  • @bamh1re318
    @bamh1re318 Před měsícem

    Great presentation, thanks! How many of the ~5,000 human enzymes have been targeted with clinical medicines? Is Lipinski's 'rule of five' still valid? He claimed there are ~500 enzymes considered "bottleneck" in biologically high impact nodules.

    • @sib-swissinstituteofbioinf4579
      @sib-swissinstituteofbioinf4579 Před měsícem

      UniProt is probably not the first place to start looking for drug targets, and to obtain such numbers, as this is outside our field of expertise. But there are various resources that are trying to address drug targets and which are worth exploring, although they probably all define targets and druggability slightly differently: - IDG resources (Illuminating the Druggable Genome): They assign 4 different "target development levels" to drug targets: Tclin, Tchem, Tbio or Tdark. Tclin are targets for which an approved drug exists; Tchem are proteins that are not Tclin, but are known to bind small molecules with high potency, etc... (academic.oup.com/nar/article/51/D1/D1405/6851109). The PHAROS interface can be used to query the IDG data, e.g. for Tclin and Tchem pharos.nih.gov/targets?facet=Target%2BDevelopment%2BLevel!Tclin&facet=Target%2BDevelopment%2BLevel!Tchem , and to further filter this for enzymes. - DrugBank allows filtering for targets (e.g.go.drugbank.com/releases/latest#target-sequences) or enzymes. - OpenTargets www.opentargets.org/ - Human Protein Atlas (HPA) www.proteinatlas.org/humanproteome/tissue/druggable UniProtKB has cross-references to PHAROS, DrugBank, OpenTargets and HPA, and you can explore narrowing down the set of human enzymes to those entries with cross-references to one or more of these databases. Please don't hesitate to contact the UniProt helpdesk (www.uniprot.org/contact) with questions about UniProt, or directly write to the providers of the resources listed above. The UniProt team

  • @pumla5481
    @pumla5481 Před 2 měsíci

    These videos have been very helpful, is there a part 3 ?

  • @hasantarek6521
    @hasantarek6521 Před 2 měsíci

    better quality plz

  • @zirban6434
    @zirban6434 Před 3 měsíci

    how can you do a 50% and a 70% modeling?

  • @AlgoNudger
    @AlgoNudger Před 4 měsíci

    Thanks.

  • @AlgoNudger
    @AlgoNudger Před 4 měsíci

    Thanks.

  • @user-jy8em2hi1x
    @user-jy8em2hi1x Před 5 měsíci

    Wonderful tool! Thanks a lot for cover up the opportunity!

  • @StevenNess
    @StevenNess Před 5 měsíci

    super helpful, thank you

  • @efstratioskirtsios298
    @efstratioskirtsios298 Před 6 měsíci

    Is there any video available on how to go on refining the clustering in more detail?

  • @patrickjiang402
    @patrickjiang402 Před 6 měsíci

    Thank you for this wonderful talk! It is very insightful on the current advances of physics-informed machine learning techniques in protein-ligand interactions!

  • @philippkrumm5921
    @philippkrumm5921 Před 6 měsíci

    is it possible to upload this in a better quality? Thats the most importand video from the series and its hard to read in 360p

  • @vicentcaselles4807
    @vicentcaselles4807 Před 7 měsíci

    How do you get intuitively that the p of genotype error is 0.02?? I don't understand that

    • @aleserain
      @aleserain Před 2 dny

      it is a binomial distribution formula in which 0.002 is the likelihood.

  • @MaheshJethalia
    @MaheshJethalia Před 8 měsíci

    I am an avid user of SWISS PROT and Homology models. I have used SIB software and loved them. I would have loved to visit or see in person but I trust you guys for doing an amazing job.

  • @AlgoNudger
    @AlgoNudger Před 8 měsíci

    Thanks.

  • @AnimeshSharma1977
    @AnimeshSharma1977 Před 8 měsíci

    thanks for sharing this! i see that you are analyzing group specific missing values separately from rest of data, wondering is there is an elegant way without utilizing group information?

  • @露露宋
    @露露宋 Před 9 měsíci

    I want to get the course material, but the link can't be opened. Could you please update the link?

  • @amalelfoly5944
    @amalelfoly5944 Před 9 měsíci

    I am following using the same steps but local quality estimates figure isnot porvided? what does this mean?

  • @chrisjmolina
    @chrisjmolina Před 9 měsíci

    Thank you for sharing!

  • @PraveenIloveBharat
    @PraveenIloveBharat Před 9 měsíci

    Best tutorial video. It will useful for all life science researchers. Thank you SIB.

  • @wilsonfarrell4774
    @wilsonfarrell4774 Před 9 měsíci

    Promo`SM ☀️

  • @ruruyang914
    @ruruyang914 Před 10 měsíci

    When you introduce each method, it will be great and helpful to give a comments or recommendations for each modality.

  • @AlgoNudger
    @AlgoNudger Před 10 měsíci

    Thanks.

  • @user-oh1zc8qt6i
    @user-oh1zc8qt6i Před 10 měsíci

    👍👍

  • @saubaral
    @saubaral Před 11 měsíci

    i love this :)😄😄

  • @Matladi474
    @Matladi474 Před rokem

    I am new to bioinformatics, my question is what if % identity and Query coverage is less but the GMQE and Qmean score is good?, which factors are more important than the other when deciding on a good model? Again what does it mean when your swiss model has no QSQE score?

  • @life7294
    @life7294 Před rokem

    anyone can please tell me the scope of bioinformatics? how can we professionally work in this field?

  • @user-hy6vn7no6j
    @user-hy6vn7no6j Před rokem

    Where can we access the swiss_census_1880.csv?

  • @hmzkha01
    @hmzkha01 Před rokem

    What are the criterias to get job in SIB

  • @chitarnjansahu473
    @chitarnjansahu473 Před rokem

    I have KYC my account but still my money is not coming out please help me

  • @eujebenqo6159
    @eujebenqo6159 Před rokem

    Bioinformatics is soo cool.

  • @kajalpanchal8239
    @kajalpanchal8239 Před rokem

    loved the vedio, Artistic!

  • @edwardsedwards796
    @edwardsedwards796 Před rokem

    Epidemics? So you are part of this scam as well? Shame on you.

  • @CMunsk
    @CMunsk Před rokem

    Thank you very much for the excellent and informative video

  • @HadasAshkenazi-eg9mn

    Thank you! Very informative

  • @ShakespeareCafe
    @ShakespeareCafe Před rokem

    Invest in some better audio equipment

    • @naromsky
      @naromsky Před 10 měsíci

      The audio quality is poor, but it could be improved with an AI enhancement (post factum).

  • @sanashaheen6864
    @sanashaheen6864 Před 2 lety

    plz explain the repository portion in swiss model

  • @AnimeshSharma1977
    @AnimeshSharma1977 Před 2 lety

    Double descent discussed at czcams.com/video/kCodNz3IHhU/video.html is enlightening and scary at the same time!

  • @langleywright2647
    @langleywright2647 Před 2 lety

    hahahaaha

  • @jovialcs-it1387
    @jovialcs-it1387 Před 2 lety

    Kudos keep doing👍

  • @kasra01
    @kasra01 Před 2 lety

    A fun and to-the-point video. Nice job

  • @salah-dred8576
    @salah-dred8576 Před 3 lety

    Wow, this video makes me a proud bioinformatian ,👨‍🔬

  • @musicspinner
    @musicspinner Před 3 lety

    Does the peptide uniqueness check consider proteolytic sites? (e.g. a match against all theoretical tryptic peptides for the human proteome?) Or is it simply matching the peptide sequences against intact protein sequences? Thanks.

  • @omarpaez5990
    @omarpaez5990 Před 3 lety

    Hi. I have been trying to model a fusion protein in Swiss-Model and havent suceeded. The template search only allows selection among the top 50 templates (and all happen to be the same protein) and although the complete list of templates is shown in html and .txt those lists are only descriptive ... In the "USER TEMPLATE" mode I have not succeeded either. This mode permits uploading 2 templates indeed but the model is based on just one of the templates... I need a model of the fusion protein based on the PDBs of the two proteins that are fused in my target sequence.

    • @sib-swissinstituteofbioinf4579
      @sib-swissinstituteofbioinf4579 Před 3 lety

      Dear Omar, Thank you for reaching out. We would recommend you to contact directly the group that has developed Swiss-model: www.sib.swiss/torsten-schwede-group. You can find their contact details on the webpage. Best regards, SIB Communication Team

  • @nishantthalwal4530
    @nishantthalwal4530 Před 3 lety

    This is literally heaven for me.

  • @Xotna-bv8pj
    @Xotna-bv8pj Před 3 lety

    WOW, this is definitely the most coolest things kinda movie trailer about computer science!

  • @KonstantinOkonechnikov

    Nice video, but it's only the first part of lecture if I understood correctly. Where is the second?

    • @sib-swissinstituteofbioinf4579
      @sib-swissinstituteofbioinf4579 Před 3 lety

      Dear Konstantin, thank you for your question and interest. This is right. The missing part, which are the practical exercises, are not in CZcams. This part is only accessible by following the course with our trainers. Here is the page where you can find the upcoming courses: www.sib.swiss/training/upcoming-training-courses Best regards, SIB Team

  • @Po0pypoopy
    @Po0pypoopy Před 3 lety

    I wish God made me as smart as these people so I could do amazing science :(

    • @luisdiaz1997
      @luisdiaz1997 Před 2 lety

      These models are very simple and common in systems biology. It's so simple is beautiful and elegant.

    • @MegaGmail007
      @MegaGmail007 Před rokem

      man I understand what you mean. Keep it up!