AI Biology & Docking
@djplabdyn.bsky.social
Confronting the AI Revolution in Structural Biology, Molecular Dynamics, and Drug Design
Conformational landscape adaptations enable processive phosphorylation by Src family kinases | Science www.science.org/doi/10.1126/...
Conformational landscape adaptations enable processive phosphorylation by Src family kinases
Processive phosphorylation by kinases enables the rapid multisite modification of signaling hubs, serving to integrate signals during time-sensitive cellular events. To achieve processivity, multiple ...
www.science.org
December 20, 2025 at 6:15 PM
Conformational landscape adaptations enable processive phosphorylation by Src family kinases | Science www.science.org/doi/10.1126/...
Going Head-to-Head with AlphaFold3 ...
Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER - Nature Biotechnology
Protein structures are predicted by integrating deep learning potentials with iterative threading fragment assembly simulations.
www.nature.com
May 29, 2025 at 1:42 PM
Going Head-to-Head with AlphaFold3 ...
Reposted by AI Biology & Docking
AI system FragFold predicts protein fragments that can bind to or inhibit a target, offering potential therapeutic applications and advancing biological research. Developed by MIT researchers, it leverages AlphaFold to predict fragment inhibitors with high accuracy. #ai (8)
AI system predicts protein fragments that can bind to or inhibit a target
FragFold, developed by MIT Biology researchers, is a computational method with potential for impact on biological research and therapeutic applications.
news.mit.edu
February 22, 2025 at 4:30 PM
AI system FragFold predicts protein fragments that can bind to or inhibit a target, offering potential therapeutic applications and advancing biological research. Developed by MIT researchers, it leverages AlphaFold to predict fragment inhibitors with high accuracy. #ai (8)
Alphafold contraints molecular dynamics simulations to give structural ensemble of [disordered proteins](www.nature.com/articles/s41...)
AlphaFold prediction of structural ensembles of disordered proteins - Nature Communications
Here, the authors introduce AlphaFold-Metainference, which uses inter-residue distances predicted by AlphaFold to generate structural ensembles of disordered proteins.
www.nature.com
February 19, 2025 at 4:53 PM
Alphafold contraints molecular dynamics simulations to give structural ensemble of [disordered proteins](www.nature.com/articles/s41...)
Gromacs 2025.0 provides basic support for running simulations with Neural Network Potential (NNP) [models](manual.gromacs.org/current/refe...
[TorchAny FF](raw.githubusercontent.com/aiqm/torchan...)
[TorchAny FF](raw.githubusercontent.com/aiqm/torchan...)
February 17, 2025 at 5:02 PM
Gromacs 2025.0 provides basic support for running simulations with Neural Network Potential (NNP) [models](manual.gromacs.org/current/refe...
[TorchAny FF](raw.githubusercontent.com/aiqm/torchan...)
[TorchAny FF](raw.githubusercontent.com/aiqm/torchan...)
Reposted by AI Biology & Docking
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
🧵
bit.ly/plaid-proteins
🧵
December 6, 2024 at 5:44 PM
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
🧵
bit.ly/plaid-proteins
🧵
Computational design of serine hydrolases | Science www.science.org/doi/10.1126/...
AI ensemble generation and "diffusion" achieve a 96,000-fold increase in engineered enzyme efficiency.
AI ensemble generation and "diffusion" achieve a 96,000-fold increase in engineered enzyme efficiency.
Computational design of serine hydrolases
The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of ...
www.science.org
February 16, 2025 at 9:59 AM
Computational design of serine hydrolases | Science www.science.org/doi/10.1126/...
AI ensemble generation and "diffusion" achieve a 96,000-fold increase in engineered enzyme efficiency.
AI ensemble generation and "diffusion" achieve a 96,000-fold increase in engineered enzyme efficiency.
Conformational ensembles reveal the origins of serine protease catalysis | Science www.science.org/doi/10.1126/...
How molecular dynamics accounts for enzymatic efficiency: a meta analyses of Xray structures.
How molecular dynamics accounts for enzymatic efficiency: a meta analyses of Xray structures.
Conformational ensembles reveal the origins of serine protease catalysis
Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes acr...
www.science.org
February 16, 2025 at 9:40 AM
Conformational ensembles reveal the origins of serine protease catalysis | Science www.science.org/doi/10.1126/...
How molecular dynamics accounts for enzymatic efficiency: a meta analyses of Xray structures.
How molecular dynamics accounts for enzymatic efficiency: a meta analyses of Xray structures.
For years, my role teaching this advanced structural biology course involved chronicling the gradual progress in computational biology...
November 23, 2024 at 2:14 PM
For years, my role teaching this advanced structural biology course involved chronicling the gradual progress in computational biology...