Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D相似文献   

A comparison of heuristic search algorithms for molecular docking

This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein–ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone.     

A generator of protein folding kinetics states for the diffusion–collision model

Two separate algorithms for calculating the intermediate states, using cellular automata, and the initial conditions in the rate matrix for the diffusion–collision model are introduced. They enable easy and fast calculations of the folding probabilities of the intermediate states, even for a very large number of microdomains. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 923–932, 2000     

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

Implicit solvent models for biomolecular simulations have been developed to use in place of more expensive explicit models; however, these models make many assumptions and approximations that are likely to affect accuracy. Here, the changes in free energies of solvation upon folding of several fast folding proteins are calculated from previously run μs–ms simulations with a number of implicit solvent models and compared to the values needed to be consistent with the explicit solvent model used in the simulations. In the majority of cases, there is a significant and substantial difference between the values calculated from the two approaches that is robust to the details of the calculations. These differences could only be remedied by selecting values for the model parameters—the internal dielectric constant for the polar term and the surface tension coefficient for the nonpolar term—that were system‐specific or physically unrealistic. We discuss the potential implications of our findings for both implicit and explicit solvent simulations. © 2015 Wiley Periodicals, Inc.     

New angle‐dependent potential energy function for backbone–backbone hydrogen bond in protein–protein interactions

Backbone–backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein–protein complex. Here, we propose an angle‐dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy funtion is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard‐Jones 12‐10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge‐based potential derived by applying Boltzmann statistics for a variety of protein–protein complexes in protein data bank. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Complete one‐ and two‐center partitioning scheme for the total energy in the Hartree–Fock theory

We proposed a complete calculation scheme for attributing the total energy by the Hartree–Fock theory to atoms (E_A) and the region between two atoms (E_AB). It was pointed out that the conventional method using the Fock matrix includes a large amount of mutual contamination in both E_A and E_AB. The new scheme was derived from the basic expression of the total energy. Calculated results by the new scheme satisfy the theoretical requirements. The scaling effect on partitioned energies was also examined. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 35–46, 1999     

NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions

The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson–Hasselbalch‐based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd.