9 papers
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation
Jes Frellsen, Maher M. Kassem, Tone Bengtsen +4
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse…
Integrative modelling of biomolecular dynamics
Daria Gusew, Carl G. Henning Hansen, Kresten Lindorff-Larsen
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or…
Computational design of intrinsically disordered proteins
Giulio Tesei, Francesco Pesce, Kresten Lindorff-Larsen
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the…
Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
Hamidreza Ghafouri, Pavel KadeÅávek, Ana M Melo +23
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature…
How to use quantum computers for biomolecular free energies
Jakob Günther, Thomas Weymuth, Moritz Bensberg +18
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide ran…
Software package for simulations using the coarse-grained CALVADOS model
Sören von Bülow, Ikki Yasuda, Fan Cao +6
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using th…