Related papers: Protein simulations combining an all-atom force fi…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
We report a novel Monte Carlo scheme that greatly enhances the power of parallel-tempering simulations. In this method, we boost the accumulation of statistical averages by including information about all potential parallel tempering trial…
We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Go model. The potential energies and vibrational free energies of inherent structures are…
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…
The simple genetic algorithm is proposed for the simulation of quantum many body dynamics. It uses the selection of entangled quantum states and has the inbuilt absolute decoherence that comes from the limitation of classical memory. It…