Simulation of Linear and Cyclic Alkanes with Second-Order Møller-Plesset Perturbation Theory through Adaptive Force Matching.

Predicting ensemble properties, such as density and heat of vaporization, of small hydrocarbons is challenging due to the dispersion-dominated weak interactions between these molecules. With the adaptive force matching (AFM) method, the bonded and short-range nonbonded interactions are fitted to second-order Møller-Plesset perturbation theory (MP2) references computed with the def2-TZVP basis set. The dispersion is modeled using symmetry adapted perturbation theory (SAPT) at MP4 accuracy using the def2-TZVPD basis set.

Effective Local and Secondary Protein Structure Prediction by Combining a Neural Network-Based Approach with Extensive Feature Design and Selection without Reliance on Evolutionary Information.

Protein structure prediction continues to pose multiple challenges despite outstanding progress that is largely attributable to the use of novel machine learning techniques. One of the widely used representations of local 3D structure-protein blocks (PBs)-can be treated in a similar way to secondary structure classes. Here, we present a new approach for predicting local conformation in terms of PB classes solely from amino acid sequences.

Method of kinetic characterization of immunoreagents for development of express high-sensitive assays for detection of ochratoxin A and heart fatty acids binding protein.

Development of rapid and sensitive immunoassays is a task of great importance in a variety of fields ranging from clinical practice and urgent diagnostics to food quality control and environmental monitoring. High attention of researches is paid to methods of screening, selection, and kinetic characterization of antibodies that enable fast, specific, and effective formation of immunocomplexes. Herein, we present a method for direct investigation of kinetics of immunoreagents during developments of express high sensitive lateral flow assays.

Structural coordinates: A novel approach to predict protein backbone conformation.

Motivation: Local protein structure is usually described via classifying each peptide to a unique class from a set of pre-defined structures. These classifications may differ in the number of structural classes, the length of peptides, or class attribution criteria. Most methods that predict the local structure of a protein from its sequence first rely on some classification and only then proceed to the 3D conformation assessment.

Partial charges for molecular-mechanical models of heterocyclic compounds: pyridine nitrogen.

This paper deals with the effect of introducing an additional interaction site onto molecular-mechanical models of nitrogen-containing heterocyclic compounds. The introduction of only one additional site next to nitrogen atoms is shown to result in significant improvement of the quality of the models along with negligible slowdown of calculation speed. Concretely, it was proposed to introduce the site inside the aromatic ring at a distance of 0.

To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC.

A more efficient version of the Expanded Ensembles method for calculation of free energy in molecular-mechanical simulations is proposed. The method is based on the Horowitz L2MC approach to accelerate movement along the "alchemical" coordinate. It is possible to achieve the same efficiency of the algorithm both with the optimal number of "windows" and with a larger number of them compared to the original algorithm.

Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances.

Application of a small radius of the hydrogen atom in molecular-mechanical models of hydrogen bonding improves the estimate of the solvation free energy of organic substances. At the same time, the density and evaporation heat of the bulk water vary slightly and are close to experimental values. Blind testing drug candidates in the SAMPL6 simulation competition showed that using the same Lennard-Jones hydrogen parameters for the hydroxyl, hydroxycarbonyl, amino, and amide groups is enough to predict log P octanol-water with MAE 0.

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction.

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges.

AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes.

A molecular mechanics force field of the AMBER/OPLS family for perfluoroalkanes, noble gases, and their mixtures with alkanes has been proposed. We had to abandon the traditional Lorentz-Berthelot combining rules for the Lennard-Jones potential to be able to uniformly describe these substance classes and their mixtures. Instead, the Waldman-Hagler rules developed for noble gases were used for all of these elements except hydrogen.

Studying progression from glucose intolerance to type 2 diabetes in obese children.

Aim: Identification of metabolic and genetic factors capable to mediate progression from normal glucose tolerance (NGT) through impaired glucose tolerance (IGT) to type 2 diabetes (T2D) in childhood obesity.

Patients And Methods: Three groups of obese children with NGT (n=54), IGT (n=35), and T2D (n=62) were evaluated. A control group of non-obese normal children (n=210) was also studied.

A new AMBER-compatible force field parameter set for alkanes.

We present a new force field parameter set for simulating alkanes. Its functional form and parameters are chosen to make it directly compatible with the AMBER94/99/12 family of force fields implemented in the available software. The proposed parameterization enables universal description of both the conformational and thermodynamic properties of linear, branched, and cyclic alkanes.

Modification of the CHARMM force field for DMPC lipid bilayer.

The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations.

New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures.

A new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic charges were calculated from a high level ab initio theory and finally the Lennard-Jones parameters were tuned to fit the experimental density and evaporation heat. The obtained in this way model reproduces correctly densities of water-acetonitrile mixtures as well as provides qualitative description of the dielectric permittivity and self-diffusion coefficients.

Nanoporous carbide-derived carbon with tunable pore size.

Porous solids are of great technological importance due to their ability to interact with gases and liquids not only at the surface, but throughout their bulk. Although large pores can be produced and well controlled in a variety of materials, nanopores in the range of 2 nm and below (micropores, according to IUPAC classification) are usually achieved only in carbons or zeolites. To date, major efforts in the field of porous materials have been directed towards control of the size, shape and uniformity of the pores.