60 citations · 70 across the 4 of their papers we have counts for
4 papers
Generalization Beyond Benchmarks: Evaluating Learnable Protein-Ligand Scoring Functions on Unseen Targets
Jakub Kopko, David Graber, Saltuk Mustafa Eyrilmez +4
As machine learning becomes increasingly central to molecular design, it is vital to ensure the reliability of learnable protein-ligand scoring functions on novel protein targets.…
Visual Support for the Loop Grafting Workflow on Proteins
Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias +5
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzi…
sMolBoxes: Dataflow Model for Molecular Dynamics Exploration
Pavol Ulbrich, Manuela Waldner, Katarína Furmanová +4
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a fra…
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport
Jiří Filipovič, Ondřej Vávra, Jan Plhák +5
Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algo…