The bumbling biochemist (Bri Bibel)
@bumblingbiochemist.bsky.social
Assistant Prof of Biochemistry & Chemistry @ LMU | Metabolic enzymes of bioremediating bacteria. Making biochemistry fun & accessible #biochemsky #chemsky http://thebumblingbiochemist.com/ & https://www.youtube.com/@thebumblingbiochemist
Core biochemistry toolbox: software, databases, etc. to get familiar with . . .The exact programs and tools you will need will depend on your project, but these are some core ones most biochemists will need. youtu.be/lEwtO5cJPwM
Core biochemistry toolbox: software, databases, etc. to get familiar with
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Resources, software, and databases for studying proteins. I just updated my protein resources guide with a video tour and downloadable PDF youtu.be/nvZGsBim5Uw
Resources, software, and databases for studying proteins
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The UniProt basket helps you quickly re-find and work with sequences/ entries you're interested in and the toolbox helps you quickly view, modify, and/or rerun alignments, BLASTs, and ID mappings. youtu.be/sWUIUgp2Ak4
UniProt Basket and Toolbox
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UniProt makeup - UniProtKB vs UniRef vs UniParc. . . youtu.be/uXbwNHnhVoA
UniProt makeup - UniProtKB vs UniRef vs UniParc
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Without annotations, sequence data is only as useful as a "map" without lines or labels youtu.be/z2vyZ6bfGkg
Annotations of sequence data (proteins, chromosomes, genes, etc.), especially UniProt
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Probably my all-time favorite book . . . Breath from Salt: A Deadly Genetic Disease, a New Era in Science, and the Patients and Families Who Changed Medicine Forever by Bijal P. Trivedi, 2020 youtu.be/o7UzGvvl6Bw
Probably my all-time favorite book: Breath from Salt by Bijal Trivedi
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The PDB allows you to group structures by % sequence similarity or Uniprot accession. This helps you quickly explore structures within & between groups of closely or more distantly related proteins. Or find the "best" structures of a specific protein for your needs. youtu.be/07gRZXI5uCU
Grouping structures in the PDB
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Another another reason to love the PDB! @rcsbpdb.bsky.social The PDB Pairwise Structure Alignment tool aligns one or more structures (experimentally-determined or predicted) and their sequences to a reference structure and sequence based on their shapes. youtu.be/MOBMBuAIAKo
Pairwise Structure Alignment of protein structures through the PDB
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Basics of cryo-EM map interpretation and validation. youtu.be/G57aBLsBgOk
Basics of cryo-EM map interpretation and validation
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Wondering what those red and green blobs are in x-ray crystallography figures? I've got your back... youtu.be/zHNwT23q4u4
Overview & practical guide to x-ray crystallography maps (2fo-fc, fo-fc (difference map), omit maps)
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Base Editing (BE) is a form of CRISPR/Cas gene editing that uses nucleotide deaminases to alter single nucleotide bases (letters) in DNA sequences (make point changes). Here’s a walk/talk-through of the 2016 paper that introduced base editing to the world. youtu.be/g90ThBinzuo
Base editing - overview and deep dive into the 2016 paper introducing it to the world
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The CCP4 bulletin board is the place to be if you're interested in x-ray crystallography! youtube.com/shorts/zK_KX...
The CCP4 bulletin board is the place to be if you're interested in x-ray crystallography
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With over a quarter million structures, how do you actually find what you’re looking for in the PDB? One way is the Advanced Search Query Builder in the PDB, which allows you to search based on similar sequences, structures, motifs, experimental methods, ligands, etc. youtu.be/iSM6orTve-Y
Advanced Search in the PDB (Protein Data Bank)
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Even when it’s not actually “Table 1,” crystallographers often use the term “Table 1” to refer to the table of statistics used to report the quality of their structural model and the underlying data, as well as some of the parameters about how the data was collected & processed. youtu.be/ewGz-O7dAS0
Interpreting "Table 1" crystallography data
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One more reason to love the @rcsbpdb.bsky.social? A hidden gem in the PDB: The 3D Sequence Annotation Viewer! youtu.be/6zKBBkzl-4A
PDB 3D Sequence Annotation Viewer for exploring features of protein etc. structures, examples
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How do you know if a structural model is reliable? Assessing the quality of a structural model through PDB validation reports and quality measures youtu.be/0AswlZBLpKw
Assessing the quality of a structural model through PDB validation reports and quality measures
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CRISPR/Cas12a2, what’ll it do? Use an RNA guide to target and destroy specific cells for you! Paper walk/talk-through on articles exploring use of the CRISPR-Cas12a2 system in eukaryotic cells youtu.be/akLmNkQz4_E
Paper walk/talk-through on articles exploring use of the CRISPR-Cas12a2 system in eukaryotic cells
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Getting up to speed & staying up to date in a field, finding & organizing papers, taking notes, etc. youtu.be/kec8k4SYAl4
Getting up to speed & staying up to date in a field, finding & organizing papers, taking notes, etc.
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Tips for taking quick notes during a literature review or similar - be sure to note your sources! youtu.be/JCYJV0JCGDc
Advice for taking quick notes during a literature review or similar - be sure to note your sources!
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What's in the PDB? A LOT! An exploration of Protein Data Bank statistics youtu.be/2Z34AeHhQUs
What's in the PDB? A LOT! An exploration of Protein Data Bank statistics
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Assemblies, asymmetric units, models & unit cells oh my! Different PDB views of crystal structural models youtu.be/WARocabgfWM
Assemblies, asymmetric units, models & unit cells oh my! Different PDB views of crystal structures
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Protein structural representation styles - what, why, and how we show protein structural models in different styles youtu.be/KqT4vrMOHNY
Protein structural representations & showing them in PyMOL
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Some of the earliest genetic sleuthing was done to figure out the cause of cystic fibrosis. The techniques discovered to do it were later used to figure out the cause of other diseases including Huntington’s Disease and hereditary breast cancer. Much more here: bit.ly/cysticfibros...
Cystic fibrosis science: history, present, & future
You might not stop to think about it much, especially with all the talk of coronavirus transmission, but it’s pretty amazing that people don’t get more respiratory infections. We’re constantly breathi...
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Book recommendations related to genetic/genomic mapping and/or testing... youtu.be/39J5ihyIMtI
Books recommendations about genetic and/or genomic mapping and/or testing
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There's a lot of weirdness in academic science, so it's totally normal to be confused. I strongly believe this shouldn't hold you back! So this my attempt to help. Hope it does! youtu.be/gC3X1PCzxpo
Demystifying the hidden curriculum of academic science - resources
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Burnout is an occupational hazard of academic science - be sure to take time to disconnect from your work, ideally short regular breaks as part of your normal routine, so you don’t have to take a crash day.... youtube.com/shorts/47wjy...
Burnout
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The freshness of your protein samples could be key to their crystallization! Some practical tips... youtu.be/0gGufXqlGGI
The freshness of your protein samples could be key to their crystallization - some tips
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Heterogeneous nucleation & tips for checking protein crystallization drops & playing crystal or crud youtu.be/nHVdpjIerG0
Heterogeneous nucleation & tips for checking protein crystallization drops & playing crystal or crud
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Continuing the hidden curriculum of academic science thread. . . There are often many "right" ways to do the same overall lab experiment & different labs often do things in different ways (different protocols, equipment, buffers, etc.) based on what they have &/or know. youtu.be/bMQwIp13cas
There are often many "right" ways to do the same overall lab experiment
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