Knowing the structure of proteins is an essential step in developing new medicines. This is a very time consuming and expensive process. Researchers from many different areas are trying to find new and efficient ways to discovery protein structures. This is known as the Protein Structure Prediction (PSP) problem and it is divided into experimental and in silico methods [3]. In this work, we use...

Does aqueous solvent discriminate among peptide conformers? To address this question, we computed the solvation free energy of a blocked, 12-residue polyalanyl-peptide in explicit water and analyzed its solvent structure. The peptide was modeled in each of 4 conformers: alpha-helix, antiparallel beta-strand, parallel beta-strand, and polyproline II helix (P(II)). Monte Carlo simulations in the ...

This paper applies the Bayesian Model Averaging statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from empirical statistical models to ab initio quantum mechanical approaches. Each of these methods is based on a set of conceptual assumptions that can affect predictive accu...

Computational methods available for the calculation of relative and absolute binding affinities (free energy simulations, continuum electrostatics, linear interaction energy approximations, and empirical solvation models) are reviewed together with recent applications to biological systems. The decomposability of the binding free energy into physically meaningful components is examined and resu...

The H-bond inventory approach is used commonly to interpret data involving changes in the number or types of protein hydrogen bonds. I point out here that this approach gives an incorrect answer either for the standard free energy or enthalpy of the reaction between simple amides and water. On the other hand, an electrostatic solvation approach fits almost within error the polar solvation free ...

A novel set of 3D descriptors, based on local grid-based COSMO s-profiles (LSPs), has been recently proposed as a promising alternative to force-field based MIFs in 3DQSAR [1]. These descriptors are grounded in the quantum chemistry-based COSMO-RS theory, which has become one of the methods of choice for the prediction of fluid phase equilibrium constants (e.g., partition coefficients, solubili...

Quantum mechanical calculations of different energies components of 1,10-phenanthroline in ground state were carried out by DFT method , in isolated state and in various solvents to study the effects of solvents on various energy components . The solvation energy, chemical potential, hardness, electrophilicity of 1,10-phenanthroline were calculated with the help of computed HOMO-LUMO gap of 1,1...

      In this study, the interaction between NO2+ cation and Hen (n = 1-7) clusters is investigated by means of ab initio calculations at MP2/aug-cc-pVTZ and QCISD/aug-cc-pVTZ computational levels. The first and second solvation shells were obtained while N atom of NO2+ interacts with five and two He atoms, respectively. Stabilizat...

the molecular dynamics (md) simulation method is used to assess structural details for humanprion protein (hereafter prpn) and its asp178 asn mutant (hereafter prpm) which causes fatalfamilial insomnia disease. the results reveal that the flexibility and instability increase in prpmcould be related to specific amino acids exposed to the solvent. solvation free energy of prpm is 20kjmot1nni2 mor...