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We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
Most human proteins remain undrugged, over 96% of human proteins remain unexploited by approved therapeutics. While structure-based virtual screening promises to expand the druggable proteome, existing methods lack atomic-level precision…
Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
Drug discovery seeks molecules (ligands) that bind strongly and selectively to a target protein. However, fewer than 5% of candidate ligands pass the bar for even the early stages of drug discovery. Furthermore, we want methods that work…
The dynamic mode decomposition (DMD) is a simple and powerful data-driven modeling technique that is capable of revealing coherent spatiotemporal patterns from data. The method's linear algebra-based formulation additionally allows for a…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
The Protein Data Bank (PDB) contains more than 135 000 entries today. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, mostly solid state NMR-recorded amyloid structures are…
The dynamics of energetic particle (EP) species, born from fusion reactions or plasma heating schemes, are critical for predicting the behavior of magnetic confinement fusion experiments and future fusion reactors. Because energetic…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…