Related papers: An effective all-atom potential for proteins
Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single…
We introduce "bond-counting" potentials, which provide an elementary description of covalent bonding. These simplistic potentials are intended for studies of the mechanisms behind a variety of phase transitions in elemental melts, including…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
In this work, we developed an interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a reactive semi-empirical many-body potential based on density functional theory and pair potentials. We…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
We apply the general protocol of parameter optimization (Lee, J. et al. Phys. Chem. B 2001, 105, 7291) to the UNRES potential. In contrast to the earlier works where only the relative weights of various interaction terms were optimized, we…
Recent advances in machine-learned interatomic potentials largely benefit from the atomistic representation and locally invariant many-body descriptors. It was however recently argued that including three- (or even four-) body features is…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…
A new scheme for constructing approximate effective electron potentials within density-functional theory is proposed. The scheme consists of calculating the effective potential for a series of reference systems, and then using these…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
Computational protein design has a wide variety of applications. Despite its remarkable success, designing a protein for a given structure and function is still a challenging task. On the other hand, the number of solved protein structures…
In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic…