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#500QueerScientists #QueerinSTEM #STEMPride #pridemonth #Pride2018 500queerscientists.com/fullscreen-pag

Jun 12, 2018

Sometimes young LGBTQ+ STEM students don't think there are other scientists like them. There are lots, including me. Some of us have even been around for quite awhile :-).

@500QueerSci

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Since it’s #Pride2023, it’s a good time to announce this! With the help of

@Jquintanalcala

and

@Alex_Cocker89

, we’re launching our next immunology seminar series, starting late September. As always, the aim is to showcase research from LGBTQ+ immunologists! 🏳️‍⚧️🌈🏳️‍🌈 #LGBTQSTEM

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DDMut: predicting effects of mutations on protein stability using deep learning academic.oup.com/nar/advance-ar

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Jun 7

I always tell my students in structural bioinformatics - read what Janet wrote about their topic 10,20, 30, or 40 years ago. She had great insights even with a lot less data than we have.

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Wolfgang Huber

@wolfgangkhuber

Jun 7

Today @EMBL marks a celebration for Janet Thornton, one of world's leading researchers in structural bioinformatics, @EMBLEBI director 2001-15, and just an amazing leader, role model, mentor and person. On the occasion of her retirement from duties @EMBL.

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

Jun 6

...and of course -- info missing from AF2 structures that is only present in experimental structures. 1.5/3

My take on good AF2: it's like crystallography/cryo-EM. You can get good biological insights with the right protein constructs. In both AF2 and experiments, they can be too short (missing important structure) or too long (stuff getting in the way of the biological interactions).

Both AF2 and experimental structures can have artifacts due to constructs that provide misleading answers or don't answer the important biological questions.

(3) Structures that would be difficult by crystallography or cryo-EM - e.g. small folded elements of a long IDR that interact with a folded protein. In this case, model explained much prior experimental data. Construct would be hard to identify & too unstable for experiments. 3/3

Examples: (1) N/C terminal tails not included in crystal construct but clearly interact with the folded protein (corroboration from experimental structures of homologues). (2) Disulfides in AF2 model but missing from exp. structure done in inappropriate reducing conditions. 2/3

Yes, we should always state the source and input to a structure. But I have seen AlphaFold predicted structures that contain more relevant chemical and biological information than experimental structures of the same proteins. 1/3

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Karolin Luger

@LugerLab

Jun 5

I think we need a good way to distinguish alpha fold predictions from experimental, refined and validated structures. Opinions?

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All you need is love

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Our latest work on active site modularity, and final part of my PhD journey at the Thornton group, is now online! Check it out here 👇👇 biorxiv.org/content/10.110 #Bioinformatics #Structural_biology #Enzymes #Proteins

Enzyme catalysis is governed by a limited toolkit of residues and organic or inorganic co-factors. Therefore, it is expected that recurring residue arrangements will be found across the enzyme space,...

Florida Board Of Education Bans Any Mention Of Outside World bit.ly/3qnecsJ

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Jun 4

You can help Eli and Lucas leave the hell that Florida has become for trans people. gofund.me/5bbdb81c apnews.com/article/florid

When gay men were fighting for their rights, one of the main talking points from bigots was that they were pedophiles looking for young boys. The same arguments are being dragged up now against trans people. It wasn’t true then and it isn’t true now.

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Machine Learning for Ancient Languages: A Survey

Jun 4

Really - I have 20 Mbytes of data and got this.

Seriously, you can't handle more than 5 Mb of data.

Apparently you can't do much more than 1000 references at a time. Why do academics tolerate such poor performance from publishing companies?

It's impossible to upload a whole library. Why do we pay you money for such crappy software?

EndNote Online sucks. Refuses to import more than a couple hundred references at a time.

Refusing to call someone by the name they want or the pronoun they feel reflects them best is the very definition of being an asshole for no other reason than wanting to be an asshole. Hurting someone just to hurt them, with no other benefit than wanting them to feel bad.

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📚 Special thanks to co-authors

@Avra_b

@napoles3D

@Mitch_P

and Roland who made it possible to release this book chapter on Building #bioinformatics web apps with

@streamlit

We share our best practices and collate use cases in the field 🔎 Preview books.google.co.th/books?id=MgCoE

New article on machine learning applications to Ancient languages, by

@tsommerschield

@iassael

@itpavlopoulos

, Vanessa Stefanak, Andrew Senior,

, John Bodel,

Abstract. Ancient languages preserve the cultures and histories of the past. However, their study is fraught with difficulties, and experts must tackle a range of challenging text-based tasks, from...

Our MPI meeting started off successfully today #MPI2023. It's great meeting with excellent researchers and talking about the latest developments in #PPIs #docking. A number of speakers presented today, including

Where do I get a list of FDA approved drugs that are in the PDB (with official name and PDB three-letter codes)? Can't seem to find an updated list.

Our classification systems for kinases (dunbrack.fccc.edu/kincore) and antibodies (dunbrack2.fccc.edu/pyigclassify2) are well used. Hoping that our RAS classification will be similarly impactful. The RAS community hasn't quite taken it onboard yet... #KRAS

Lots of great simulation papers on RAS. We clustered and classified the experimental structures of HRAS, KRAS, and NRAS to provide a framework for comparing simulations with experiments. doi.org/10.1158/0008-5 dunbrack.fccc.edu/rascore.

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Mitchell Parker, PhD

@Mitch_P

May 21

Nice paper! Would love to conformationally classify trajectory snapshots with Rascore (dunbrack.fccc.edu/rascore/). We provide the druggable conformations from your Fig. 7 in our paper: aacrjournals.org/cancerres/arti

The age of Men is over. The time of the Orcas has come.

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Will Rinehart

@WillRinehart

May 19

Orcas have sunk 3 boats in Europe and appear to be teaching others to do the same. Scientists think a traumatized orca initiated the assault on boats after a "critical moment of agony" and that the behavior is spreading among the population. livescience.com/animals/orcas/

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And the Water Taxi to Logan Airport.

The Boston-Provincetown ferry is running again! I’ve missed it.

I'm done with going to scientific conferences in US states that ban abortion or gender-affirming care or drag shows or library books about LGBTQ lives... Where is ISMB2024 going to be?

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure...

May 16

PDB insert codes are the bane of my existence.

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data biorxiv.org/cgi/content/sh #biorxiv_bioinfo

biorxiv.org

Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The...

"Extra virgin olive oil" -- My mother's TV cooking show debut (1990)

Happy Mother's Day! This is a video of my mother on a morning cooking show in Boston in 1990 (transferred from an old VHS tape so the quality is bad). But it explains a lot about my sense of humor :-). Spoiler alert: she won the contest.

youtube.com

This is my 70 year-old Italian-American mother on TV in 1990. She was a school teacher and stole the show. This was copied from an old VHS tape so the video ...

I would really appreciate it if our IT people would stop changing the damn security settings on our network without telling us.

This thread is really clarifying about what is going on in US politics right now.

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Thomas Zimmer

@tzimmer_history

A Ciliary SMOOTHENED-GRK2-PKA Signaling Pathway Initiates Hedgehog Signal Transduction

It’s really hard to overstate how acutely dangerous this is: All strands of the Right - leading Republicans, the media machine, the reactionary intellectual sphere, the conservative base, the donor class - are openly and aggressively embracing rightwing vigilante violence.

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Tweet from @RonDeSantisFL: “We must defeat the Soros-Funded DAs, stop the Left's pro-criminal agenda, and take back the streets for law abiding citizens. We stand with Good Samaritans like Daniel Penny. Let’s show this Marine... America’s got his back.”

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ALT

Excited to present a new story focusing on how the #GPCR #SMOOTHENED activates GLI transcription factors in the primary cilium during #Hedgehog signaling! Fantastic collab with Radhika Subramanian,

@GeXuecai

, and many others.

biorxiv.org

During Hedgehog (Hh) signal transduction in development, homeostasis, and cancer, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by...

@buildmodels

May 11

Perform Improved Pairwise Structure Alignments at RCSB.org Simultaneously analyze and visualize 3D structure and 1D sequence alignments

rcsb.org

Perform Improved Pairwise Structure Alignments

Simultaneously analyze and visualize 3D structure and 1D sequence alignments