Related papers: Maximum allowed solvent accessibilites of residues…
The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
Random sequential adsorption (RSA) of various two dimensional objects is studied in order to find a shape which maximizes the saturated packing fraction. This investigation was begun in our previous paper [Cie\'sla et al., Phys. Chem. Chem.…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
Representational Similarity Analysis (RSA) is a popular method for analyzing neuroimaging and behavioral data. Here we evaluate the accuracy and reliability of RSA in the context of model selection, and compare it to that of regression.…
Sample average approximation (SAA) is a widely popular approach to data-driven decision-making under uncertainty. Under mild assumptions, SAA is both tractable and enjoys strong asymptotic performance guarantees. Similar guarantees,…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy…
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…
A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) the kinetics of the chemical reaction between…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
A significant challenge in wet lab experiments with current drug design generative models is the trade-off between pharmacological properties and synthesizability. Molecules predicted to have highly desirable properties are often difficult…
Random packings and their properties are a popular and active field of research. Numerical algorithms that can efficiently generate them are useful tools in their study. This paper focuses on random packings produced according to the random…
Representational similarity metrics are fundamental tools in neuroscience and AI, yet we lack systematic comparisons of their discriminative power across model families. We introduce a quantitative framework to evaluate representational…
We propose a new ensemble prediction method, Random Subset Averaging (RSA), tailored for settings with many covariates, particularly in the presence of strong correlations. RSA constructs candidate models via binomial random subset strategy…
Random sequential adsorption (RSA) models have been studied due to their relevance to deposition processes on surfaces. The depositing particles are represented by hard-core extended objects; they are not allowed to overlap. Numerical Monte…
Scaling law for geometrical and dynamical quantities of biological molecules is an interesting topic. According to Flory's theory, a power law between radius of gyration and the length of homopolymer chain is found, with exponent 3/5 for…
The planted coloring problem is a prototypical inference problem for which thresholds for Bayes optimal algorithms, like Belief Propagation (BP), can be computed analytically. In this paper, we analyze the limits and performances of the…