Krishna Mallipeddi
@krishnamallipeddi.bsky.social
Protein Engineering
Expected better from @anericanairlines.bsky.social @americanaircared.bsky.social! Flight cancelled yesterday takes 3h to rebook. now morning flight takes too long to fuel, no AC, no ground crew because of shift change, definitely going to miss connection with 1h delay…so far
July 30, 2025 at 9:49 AM
Expected better from @anericanairlines.bsky.social @americanaircared.bsky.social! Flight cancelled yesterday takes 3h to rebook. now morning flight takes too long to fuel, no AC, no ground crew because of shift change, definitely going to miss connection with 1h delay…so far
Reposted by Krishna Mallipeddi
I spent way too long on this but I made a small benchmark for OCR of biological sequences.
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
May 30, 2025 at 10:55 PM
I spent way too long on this but I made a small benchmark for OCR of biological sequences.
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
Reposted by Krishna Mallipeddi
Protein degradation in E. coli via N-terminal degradation signals (degrons) defined by the @kunjapur.bsky.social lab. @ispt-proteinterm.bsky.social www.biorxiv.org/content/10.1...
Combinatorial mutagenesis of N-terminal sequences reveals unexpected and expanded stability determinants of the Escherichia coli N-degron pathway
Although it is known that penultimate N-terminal residues can influence protein stability by the N-degron pathway, there has not been a comprehensive effort to document nor predict these effects for n...
www.biorxiv.org
May 23, 2025 at 2:04 PM
Protein degradation in E. coli via N-terminal degradation signals (degrons) defined by the @kunjapur.bsky.social lab. @ispt-proteinterm.bsky.social www.biorxiv.org/content/10.1...
Reposted by Krishna Mallipeddi
From Drew Lapeer @virial.bsky.social: While LLMs are certainly a useful tool in many aspects, their usage requires a level of caution. In today’s Beyond post, we’ll take a look at the best (and worst) practices for incorporating them in your scientific workflow. 🔭✨☄️
astrobites.org/2025/04/25/l...
astrobites.org/2025/04/25/l...
The Do’s and Don’ts of Incorporating LLMs into your Scientific Workflow
While LLMs are certainly a useful tool in many aspects, their usage requires a level of caution, especially when using them throughout the scientific process. In today’s Beyond post, we’ll take a look...
astrobites.org
April 26, 2025 at 10:36 AM
From Drew Lapeer @virial.bsky.social: While LLMs are certainly a useful tool in many aspects, their usage requires a level of caution. In today’s Beyond post, we’ll take a look at the best (and worst) practices for incorporating them in your scientific workflow. 🔭✨☄️
astrobites.org/2025/04/25/l...
astrobites.org/2025/04/25/l...
Reposted by Krishna Mallipeddi
I'd like to share a little bit of happy lab news in these chaotic times: a new preprint, driven by the brilliant Qinhao Cao!
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?
April 21, 2025 at 4:07 PM
I'd like to share a little bit of happy lab news in these chaotic times: a new preprint, driven by the brilliant Qinhao Cao!
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?
Reposted by Krishna Mallipeddi
The vaccine against Shingles helps protect against dementia, results of a natural experiment, adding to prior evidence
"implications are profound"
New @nature.com
www.nature.com/articles/d41...
nature.com/articles/s41...
"implications are profound"
New @nature.com
www.nature.com/articles/d41...
nature.com/articles/s41...
A natural experiment on the effect of herpes zoster vaccination on dementia - Nature
Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of...
nature.com
April 2, 2025 at 3:29 PM
The vaccine against Shingles helps protect against dementia, results of a natural experiment, adding to prior evidence
"implications are profound"
New @nature.com
www.nature.com/articles/d41...
nature.com/articles/s41...
"implications are profound"
New @nature.com
www.nature.com/articles/d41...
nature.com/articles/s41...
Reposted by Krishna Mallipeddi
Structure models generate proteins with higher structure confidence and more plausible energy distributions, but limited diversity and sequence biases. Sequence models generate diverse and novel proteins with lower structural confidence. Neither are good at generating enzymes.
March 31, 2025 at 11:22 PM
Structure models generate proteins with higher structure confidence and more plausible energy distributions, but limited diversity and sequence biases. Sequence models generate diverse and novel proteins with lower structural confidence. Neither are good at generating enzymes.
Reposted by Krishna Mallipeddi
You’ve probably heard about how AI/LLMs can solve Math Olympiad problems ( deepmind.google/discover/blo... ).
So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released.
The result: They all sucked!
So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released.
The result: They all sucked!
March 31, 2025 at 8:33 PM
You’ve probably heard about how AI/LLMs can solve Math Olympiad problems ( deepmind.google/discover/blo... ).
So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released.
The result: They all sucked!
So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released.
The result: They all sucked!
Reposted by Krishna Mallipeddi
2025 Cold Spring Harbor Laboratory Course in Synthetic Biology - apply!
Deadline: April 14, 2025
Financial Aid: Stipend awards are available.
Notifications: Applicants will be notified by May 15, 2025.
meetings.cshl.edu/courses.aspx...
Deadline: April 14, 2025
Financial Aid: Stipend awards are available.
Notifications: Applicants will be notified by May 15, 2025.
meetings.cshl.edu/courses.aspx...
Synthetic Biology
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
March 31, 2025 at 6:45 PM
2025 Cold Spring Harbor Laboratory Course in Synthetic Biology - apply!
Deadline: April 14, 2025
Financial Aid: Stipend awards are available.
Notifications: Applicants will be notified by May 15, 2025.
meetings.cshl.edu/courses.aspx...
Deadline: April 14, 2025
Financial Aid: Stipend awards are available.
Notifications: Applicants will be notified by May 15, 2025.
meetings.cshl.edu/courses.aspx...
Reposted by Krishna Mallipeddi
What an awesome group effort reporting on the structural dynamics of ~60% of available structures !!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
March 2, 2025 at 5:18 PM
What an awesome group effort reporting on the structural dynamics of ~60% of available structures !!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Krishna Mallipeddi
Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed:
Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.
Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.
February 19, 2025 at 7:30 PM
Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed:
Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.
Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.
Reposted by Krishna Mallipeddi
Hey folks--
If you're a recent (or soon-to-be) analytical chem PhD, or if you know of one...
We're hiring a 1-year VAP as sabbatical replacement. We don't do a national search for 1-year positions; it's completely word of mouth. DM me if you want details.
#ChemSky
If you're a recent (or soon-to-be) analytical chem PhD, or if you know of one...
We're hiring a 1-year VAP as sabbatical replacement. We don't do a national search for 1-year positions; it's completely word of mouth. DM me if you want details.
#ChemSky
February 13, 2025 at 4:24 PM
Hey folks--
If you're a recent (or soon-to-be) analytical chem PhD, or if you know of one...
We're hiring a 1-year VAP as sabbatical replacement. We don't do a national search for 1-year positions; it's completely word of mouth. DM me if you want details.
#ChemSky
If you're a recent (or soon-to-be) analytical chem PhD, or if you know of one...
We're hiring a 1-year VAP as sabbatical replacement. We don't do a national search for 1-year positions; it's completely word of mouth. DM me if you want details.
#ChemSky
Reposted by Krishna Mallipeddi
🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/...
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Protein codes promote selective subcellular compartmentalization
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...
www.science.org
February 8, 2025 at 11:39 PM
🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/...
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social
Reposted by Krishna Mallipeddi
Helpful table to determine how much your University or health system is set to lose if the NIH indirect cap is suddenly lowered to 15%. For SJSU it is $374k which is on the smaller end but devastating considering our other budget issues. datawrapper.dwcdn.net/l0ZqA/8/
Estimated Single Year Loss of NIH Funding if 15% Indirect Cost Rate is Imposed
Based on analysis of 2024 NIH funding data. Sums are totals of losses in funding to programs if indirect costs had been capped at 15%
datawrapper.dwcdn.net
February 9, 2025 at 4:24 PM
Helpful table to determine how much your University or health system is set to lose if the NIH indirect cap is suddenly lowered to 15%. For SJSU it is $374k which is on the smaller end but devastating considering our other budget issues. datawrapper.dwcdn.net/l0ZqA/8/
Reposted by Krishna Mallipeddi
PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
February 4, 2025 at 8:38 PM
PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
May also be the case with AF3 & Boltz-1, but haven't verified
As to what this means... see the rest of the thread 🧵
Anyone test this yet?
FlashFold: a standalone command-line tool for accelerated protein structure prediction www.biorxiv.org/content/10....
FlashFold: a standalone command-line tool for accelerated protein structure prediction
FlashFold is a fast, user-friendly tool for predicting protein structures and complexes. It can be installed locally on Linux or Mac operating systems, alleviating the computational needs, and eliminating reliance on third-party servers. FlashFold relies on a highly compact and adaptable built-in database to speed up the homology searching. Overall structure predictions are up to 3-fold faster than AlphaFold3 with sacrificing little or no accuracy. FlashFold is available at https://github.com/chayan7/flashfold.
### Competing Interest Statement
The authors have declared no competing interest.
www.biorxiv.org
January 27, 2025 at 3:18 AM
Anyone test this yet?
Reposted by Krishna Mallipeddi
Anyone figure out how to import this palette into jmp?
Having a color-blind colleague is a good reminder that we need to be more careful when designing figures for scientific publication 🧪
My lab has found this page especially useful for selecting color palettes, used in combination with different symbols: thenode.biologists.com/data-visuali...
My lab has found this page especially useful for selecting color palettes, used in combination with different symbols: thenode.biologists.com/data-visuali...
Color blind friendly palettes for data visualizations with categories
A discussion of color blind friendly palettes for labeling unique catergories in data visualization.
thenode.biologists.com
January 19, 2025 at 11:08 PM
Anyone figure out how to import this palette into jmp?
Reposted by Krishna Mallipeddi
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
January 19, 2025 at 4:40 PM
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
Reposted by Krishna Mallipeddi
FYI the designed esmGFP is 58% identical to the most similar extant GFP sequence - hence "500 million years of evolution" - but nearly half of the novelty (the 42% unaligned part of the seq) is derived from one other protein. Originally caught by @btnaughton.bsky.social, source link in alt text
January 18, 2025 at 6:42 AM
FYI the designed esmGFP is 58% identical to the most similar extant GFP sequence - hence "500 million years of evolution" - but nearly half of the novelty (the 42% unaligned part of the seq) is derived from one other protein. Originally caught by @btnaughton.bsky.social, source link in alt text
Reposted by Krishna Mallipeddi
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
November 23, 2024 at 3:50 PM
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
Reposted by Krishna Mallipeddi
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`