Trent E Balius
@dalyusbalius.bsky.social
Computational Chemist @FredNatLab. Interest are molecular docking and methods for drug discovery. Views are my own.
Reposted by Trent E Balius
There is an awesome and closely related preprint from Jiankun Lyu’s lab:
doi.org/10.64898/202... that also includes an amazing prospective σ2 head-to-head screen of AF3 vs. DOCK.
doi.org/10.64898/202... that also includes an amazing prospective σ2 head-to-head screen of AF3 vs. DOCK.
AlphaFold3 for Structure-guided Ligand Discovery
Deep-learning methods for protein structure prediction, such as AlphaFold2 (AF2) and RosettaFold (RF), have transformed structural biology and accelerated downstream biological discovery. More recent ...
doi.org
December 29, 2025 at 10:37 PM
There is an awesome and closely related preprint from Jiankun Lyu’s lab:
doi.org/10.64898/202... that also includes an amazing prospective σ2 head-to-head screen of AF3 vs. DOCK.
doi.org/10.64898/202... that also includes an amazing prospective σ2 head-to-head screen of AF3 vs. DOCK.
Reposted by Trent E Balius
Read the preprint !!! doi.org/10.64898/202...
Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens
Accurate prediction of ligand-bound protein complexes and ranking them by affinity are central problems in drug discovery. While deep learning co-folding methods can help address these challenges, the...
doi.org
December 29, 2025 at 10:37 PM
Read the preprint !!! doi.org/10.64898/202...
Further, bug fixes were implemented and additional terms were added to the descriptor scoring function. See the release note for more information: dock.compbio.ucsf.edu/DOCK_6/new_i...
dock.compbio.ucsf.edu
July 16, 2025 at 11:43 PM
Further, bug fixes were implemented and additional terms were added to the descriptor scoring function. See the release note for more information: dock.compbio.ucsf.edu/DOCK_6/new_i...
In this release, new methodologies for DOCK_DN allow users to bias fragment selection, discussed in a recent publication: onlinelibrary.wiley.com/doi/10.1002/...
Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK
Fragment-based de novo design can construct new molecules from scratch from an input library of allowable fragments and torsion types. In this work, a new series of biasing methods have been develope....
onlinelibrary.wiley.com
July 16, 2025 at 11:42 PM
In this release, new methodologies for DOCK_DN allow users to bias fragment selection, discussed in a recent publication: onlinelibrary.wiley.com/doi/10.1002/...