5 papers
Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
Mariia Ivonina, Jakub Rydzewski
The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through 1 programmed ribosomal frameshifting ( PRF), a mechanism that allo…
Decoding Binding Pathways of Ligands in Prolyl Oligopeptidase
Katarzyna Walczewska-Szewc, Jakub Rydzewski
Neurodegenerative diseases, such as Alzheimer's and Parkinson's, pose a growing global health burden. Prolyl oligopeptidase (PREP) has emerged as a potential therapeutic target in…
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
TuÄçe Gökdemir, Jakub Rydzewski
Understanding the long-time dynamics of complex physical processes depends on our ability to recognize patterns. To simplify the description of these processes, we often introduce…
A Note on Spectral Map
TuÄçe Gökdemir, Jakub Rydzewski
In molecular dynamics (MD) simulations, transitions between states are often rare events due to energy barriers that exceed the thermal temperature. Because of their infrequent occ…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…