Related papers: Asymptotic hitting time for a simple evolutionary …
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
The $(1+(\lambda,\lambda))$ genetic algorithm is a bright example of an evolutionary algorithm which was developed based on the insights from theoretical findings. This algorithm uses crossover, and it was shown to asymptotically outperform…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Evolutionary Algorithms (EAs) and other randomized search heuristics are often considered as unbiased algorithms that are invariant with respect to different transformations of the underlying search space. However, if a certain amount of…
I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and…
Despite significant empirical and theoretically supported evidence that non-static parameter choices can be strongly beneficial in evolutionary computation, the question how to best adjust parameter values plays only a marginal role in…
We consider the statistical mechanics of a full set of two-dimensional protein-like heteropolymers, whose thermodynamics is characterized by the coil-to-globular ($T_\theta$) and the folding ($T_f$) transition temperatures. For our model,…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
When a problem instance is perturbed by a small modification, one would hope to find a good solution for the new instance by building on a known good solution for the previous one. Via a rigorous mathematical analysis, we show that…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
Recent works showed that simple success-based rules for self-adjusting parameters in evolutionary algorithms (EAs) can match or outperform the best fixed parameters on discrete problems. Non-elitism in a (1,$\lambda$) EA combined with a…
Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…
Inspired by the works of Goldreich and Ron (J. ACM, 2017) and Nakar and Ron (ICALP, 2021), we initiate the study of property testing in dynamic environments with arbitrary topologies. Our focus is on the simplest non-trivial rule that can…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…