background hymenodictyon excelsum is a medicinal plant traditionally used for tumor treatment as it contains phytochemicals of anthraquinone and coumarin class. objectives the aim of the present study was to unfold the therapeutic value of selected phytocompounds of hymenodictyon excelsum in prostate cancer. materials and methods eight phytochemicals were selected based on the literature search...

Surfactant molecules are used as interesting tools to study the structure, function and stability of proteins. Protonation states of amino acids may be changed in the presence of surfactants. In this work, using experimental observations and molecular dynamic simulation, the effects of sodium dodecyl sulfate on the acid dissociation constants of tryptophan was examined. The acid–base equilibriu...

disposition and transportation of anticancer drugs by human serum albumin (hsa) affects their bioavailability, distribution and elimination. in this study, the interaction of a set of anticancer drugs with hsa was investigated by molecular dynamics and molecular docking simulations. the drugs' activities were analyzed according to their docking scores, binding sites and structural descriptors. ...

A mixing rule for the mixtures of hard-spheres is presented which can be reduced to the standard van der Waals mixing rule at low densities. The effectiveness of the mixing rule for the size and energy parameters of lennard-Jones fluid are examined by combining them with an equation of state to calculate thermodynamic properties. The results of calculation are compared with the molecular dy...

This work is conducted to obtain mechanical properties of microtubule. For this aim, interaction energy in alpha-beta, beta-alpha, alpha-alpha, and beta-beta dimers was calculated using the molecular dynamic simulation. Force-distance diagrams for these dimers were obtained using the relation between potential energy and force. Afterwards, instead of each tubulin, one sphere with 55 KDa weight ...

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures a...

Graphene sheet including single vacancy, double vacancy and Stone-Wales with armchair and zigzag structure was simulated using molecular dynamics simulation. The effect of defects on shear’s modulus, shear strength and fracture  strain was investigated. Results showed that these shear properties reduce when the degrees of all kinds of defects increase. The dangling bond in SV and DV defected gr...