chemspy.bsky.social
@chemspy.bsky.social
Reposted by chemspy.bsky.social
Preprint from the lab🚨
Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut!
Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1...
A thread 🧵
Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut!
Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1...
A thread 🧵
May 7, 2025 at 5:04 PM
Preprint from the lab🚨
Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut!
Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1...
A thread 🧵
Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut!
Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1...
A thread 🧵
Reposted by chemspy.bsky.social
Inverse folding NNs are better at predicting changes to a mutated protein's equilibrium dynamics, relative to WT, than protein folding NNs (BioEmu & AF-Cluster). This was shown on an enzyme that is more enzymatically promiscuous in the open state.
May 12, 2025 at 6:27 AM
Inverse folding NNs are better at predicting changes to a mutated protein's equilibrium dynamics, relative to WT, than protein folding NNs (BioEmu & AF-Cluster). This was shown on an enzyme that is more enzymatically promiscuous in the open state.
Reposted by chemspy.bsky.social
Designing enzymes w/ a combination of structure-based sequence design (LigandMPNN) and directed evolution. The latter step discovers unconventional mutations like a mid-helical proline, and subsequent MD simulations show an increasingly rigidified active site
De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts
De novo design of protein catalysts with high efficiency and stereoselectivity provides an attractive approach toward the design of environmentally benign catalysts. Here, we design proteins that inco...
www.science.org
May 15, 2025 at 1:25 PM
Designing enzymes w/ a combination of structure-based sequence design (LigandMPNN) and directed evolution. The latter step discovers unconventional mutations like a mid-helical proline, and subsequent MD simulations show an increasingly rigidified active site
Reposted by chemspy.bsky.social
“A joint embedding of protein sequence and structure enables robust variant effect predictions”
Combines a structure GNN w/ MSA-transformer, partly by “only allowing attention between positions in the MSA that are proximal in” 3D space
www.biorxiv.org/content/10.1...
github.com/KULL-Centre/...
Combines a structure GNN w/ MSA-transformer, partly by “only allowing attention between positions in the MSA that are proximal in” 3D space
www.biorxiv.org/content/10.1...
github.com/KULL-Centre/...
December 17, 2023 at 1:09 PM
“A joint embedding of protein sequence and structure enables robust variant effect predictions”
Combines a structure GNN w/ MSA-transformer, partly by “only allowing attention between positions in the MSA that are proximal in” 3D space
www.biorxiv.org/content/10.1...
github.com/KULL-Centre/...
Combines a structure GNN w/ MSA-transformer, partly by “only allowing attention between positions in the MSA that are proximal in” 3D space
www.biorxiv.org/content/10.1...
github.com/KULL-Centre/...
Reposted by chemspy.bsky.social
Really happy to share this iron photocatalyzed general alkene difunctionalization system developed by Kang-Jie, David, Xiaowei, Shih-Chieh, and James just published as a HOT article in Chemical Science!
pubs.rsc.org/en/content/a...
pubs.rsc.org/en/content/a...
Photocatalytic, modular difunctionalization of alkenes enabled by ligand-to-metal charge transfer an...
Ligand-to-metal charge transfer (LMCT) is a mechanistic strategy that provides a powerful tool to access diverse open-shell species using earth abundant elements and has seen tremendous growth in rece...
pubs.rsc.org
November 24, 2023 at 6:27 PM
Really happy to share this iron photocatalyzed general alkene difunctionalization system developed by Kang-Jie, David, Xiaowei, Shih-Chieh, and James just published as a HOT article in Chemical Science!
pubs.rsc.org/en/content/a...
pubs.rsc.org/en/content/a...
Reposted by chemspy.bsky.social
Altae-Tran, Kannan, Koonin, Zhang + al. reports @Science a new protein clustering algorithm + discovery of rare and previously unknown CRISPR-Cas systems - an untapped trove of diverse biochemical activities linked to RNA-guided mechanisms w/ potential for biotechnology development bit.ly/adi1910
November 25, 2023 at 7:17 PM
Altae-Tran, Kannan, Koonin, Zhang + al. reports @Science a new protein clustering algorithm + discovery of rare and previously unknown CRISPR-Cas systems - an untapped trove of diverse biochemical activities linked to RNA-guided mechanisms w/ potential for biotechnology development bit.ly/adi1910
Reposted by chemspy.bsky.social
“TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering” has been updated 🧪🧶🧬
Provides a framework to integrate PLMs, backbone diffusion, docking, inverse folding, etc
www.biorxiv.org/content/10.1...
trill.readthedocs.io/en/latest/ho...
Provides a framework to integrate PLMs, backbone diffusion, docking, inverse folding, etc
www.biorxiv.org/content/10.1...
trill.readthedocs.io/en/latest/ho...
November 11, 2023 at 11:51 AM
“TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering” has been updated 🧪🧶🧬
Provides a framework to integrate PLMs, backbone diffusion, docking, inverse folding, etc
www.biorxiv.org/content/10.1...
trill.readthedocs.io/en/latest/ho...
Provides a framework to integrate PLMs, backbone diffusion, docking, inverse folding, etc
www.biorxiv.org/content/10.1...
trill.readthedocs.io/en/latest/ho...
Reposted by chemspy.bsky.social
Today we report a new strategy for C-to-N replacement that leverages selective ring scission to turn a carbon atom into a leaving group while retaining the capacity for ring-reclosure around the nitrogen atom. Congrats to Jisoo, Colin, and Alec!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Carbon-to-nitrogen single-atom transmutation of azaarenes - Nature
A new type of transformation converting a heteroaromatic carbon atom into a nitrogen atom, turning quinolines into quinazolines to enable manipulation of molecular properties, is reported.
www.nature.com
November 1, 2023 at 4:27 PM
Today we report a new strategy for C-to-N replacement that leverages selective ring scission to turn a carbon atom into a leaving group while retaining the capacity for ring-reclosure around the nitrogen atom. Congrats to Jisoo, Colin, and Alec!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by chemspy.bsky.social
“Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling” 🧪🧶🧬
Engineering a Kemp eliminase w/ 250-fold increase in enzymatic activity using an experimental structural ensemble and molecular dynamics-based filtering
www.biorxiv.org/content/10.1...
Engineering a Kemp eliminase w/ 250-fold increase in enzymatic activity using an experimental structural ensemble and molecular dynamics-based filtering
www.biorxiv.org/content/10.1...
November 3, 2023 at 6:04 AM
“Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling” 🧪🧶🧬
Engineering a Kemp eliminase w/ 250-fold increase in enzymatic activity using an experimental structural ensemble and molecular dynamics-based filtering
www.biorxiv.org/content/10.1...
Engineering a Kemp eliminase w/ 250-fold increase in enzymatic activity using an experimental structural ensemble and molecular dynamics-based filtering
www.biorxiv.org/content/10.1...
Reposted by chemspy.bsky.social
“The genetic architecture of protein stability” 🧪🧶🧬
An additive fitness prediction model trained on ≤2 mutations predicts fitness effects of 3-13 substitutions with R2=0.5
www.biorxiv.org/content/10.1...
An additive fitness prediction model trained on ≤2 mutations predicts fitness effects of 3-13 substitutions with R2=0.5
www.biorxiv.org/content/10.1...
October 28, 2023 at 5:49 AM
“The genetic architecture of protein stability” 🧪🧶🧬
An additive fitness prediction model trained on ≤2 mutations predicts fitness effects of 3-13 substitutions with R2=0.5
www.biorxiv.org/content/10.1...
An additive fitness prediction model trained on ≤2 mutations predicts fitness effects of 3-13 substitutions with R2=0.5
www.biorxiv.org/content/10.1...
Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA - Nature Communications
Unnatural base pairing xenonucleic acids (XNAs) can be used to expand life’s alphabet beyond ATGC. Here, authors show strategies for enzymatic synthesis and next-generation nanopore sequencing of XN...
www.nature.com
October 28, 2023 at 4:00 AM
Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The self-supervised protein language models (pLMs) have demonstrated significant potential in predicting the impact of mutations. Our method shows substantial improvements in the fitness prediction tasks even using less than 200 labeled data.
openreview.net/forum?id=DUj...
openreview.net/forum?id=DUj...
Fine-tuning protein Language Models by ranking protein fitness
The self-supervised protein language models (pLMs) have demonstrated significant potential in predicting the impact of mutations on protein function and fitness, which is crucial for therapeutic...
openreview.net
October 28, 2023 at 3:59 AM
The self-supervised protein language models (pLMs) have demonstrated significant potential in predicting the impact of mutations. Our method shows substantial improvements in the fitness prediction tasks even using less than 200 labeled data.
openreview.net/forum?id=DUj...
openreview.net/forum?id=DUj...
Reposted by chemspy.bsky.social
“OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer” 🧪🧶🧬
Better prediction quality than AlphaFold2 on CASP15 targets
www.biorxiv.org/content/10.1...
github.com/OPUS-MaLab/o...
Better prediction quality than AlphaFold2 on CASP15 targets
www.biorxiv.org/content/10.1...
github.com/OPUS-MaLab/o...
October 21, 2023 at 5:53 AM
“OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer” 🧪🧶🧬
Better prediction quality than AlphaFold2 on CASP15 targets
www.biorxiv.org/content/10.1...
github.com/OPUS-MaLab/o...
Better prediction quality than AlphaFold2 on CASP15 targets
www.biorxiv.org/content/10.1...
github.com/OPUS-MaLab/o...
Reposted by chemspy.bsky.social
“Predicting a Protein's Stability under a Million Mutations” 🧪🧶🧬
Structure-based stability prediction of single- and double-point mutants
arxiv.org/abs/2310.12979
github.com/jozhang97/Mu...
Structure-based stability prediction of single- and double-point mutants
arxiv.org/abs/2310.12979
github.com/jozhang97/Mu...
October 20, 2023 at 5:09 AM
“Predicting a Protein's Stability under a Million Mutations” 🧪🧶🧬
Structure-based stability prediction of single- and double-point mutants
arxiv.org/abs/2310.12979
github.com/jozhang97/Mu...
Structure-based stability prediction of single- and double-point mutants
arxiv.org/abs/2310.12979
github.com/jozhang97/Mu...
Reposted by chemspy.bsky.social
Hmmm.....
GitHub - sokrypton/af2bind
Contribute to sokrypton/af2bind development by creating an account on GitHub.
github.com
October 17, 2023 at 12:25 PM
Hmmm.....