Related papers: Protein Folding Simulations in a Deformed Energy L…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
In recent years inelastic spin-flip spectroscopy using a lowtemperature scanning tunneling microscope has been a very successful tool for studying not only individual spins but also complex coupled systems. When these systems interact with…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We propose here some new sampling algorithms for Path Sampling in the case when stochastic dynamics are used. In particular, we present a new proposal function for equilibrium sampling of paths with a Monte-Carlo dynamics (the so-called…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
Recent innovations from machine learning allow for data unfolding, without binning and including correlations across many dimensions. We describe a set of known, upgraded, and new methods for ML-based unfolding. The performance of these…
The energy landscapes of electrostatically charged particles embedded on constant mean curvature surfaces are analysed for a wide range of system size, curvature, and interaction potentials. The surfaces are taken to be rigid, and the…
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…
We advance a combined filtered/phase-field approach to topology optimization in the setting of linearized elasticity. Existence of minimizers is proved and rigorous parameter asymptotics are discussed by means of variational convergence…
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…
We propose a new method called the N-particle underdamped Langevin algorithm for optimizing a special class of non-linear functionals defined over the space of probability measures. Examples of problems with this formulation include…
In recent years, spectral clustering has become a standard method for data analysis used in a broad range of applications. In this paper we propose a new class of algorithms for multiway spectral clustering based on optimization of a…
We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo.…
Quantum annealing is a promising approach for obtaining good approximate solutions to difficult optimization problems. Folding a protein sequence into its minimum-energy structure represents such a problem. For testing new algorithms and…
Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…
Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates retaining the beneficial properties of the original drug…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
The recent progress on global optimizations of covariant energy density functionals (CEDFs) and global calculations of binding energies within the covariant density functional theory (CDFT) has been analyzed and reviewed. Recently developed…