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...

A simulation is reliable when the simulation time is much longer than the relaxation time of the quantities in question. The aim of this work is to address the question when Molecular Dynamics (MD) simulation is reliable and how it depends on the integration algorithms and optimal time step. There were certain problems related to the choice of integration algorithms on Molecular Dynamics simula...

microtubule affinity-regulating kinase 2 (mark2) protein has a substantial role in regulation of vital cellular processes like induction of polarity, regulation of cell junctions, cytoskeleton structure and cell differentiation. the abnormal function of this protein has been associated with a number of pathological conditions like alzheimer disease, autism, several carcinomas and development of...

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...

The understanding of the dynamic behavior of distillation columns has received considerable attention because distillation is one of the most widely used unit operations in chemical process industries. This paper reports a dynamic simulation study of the possible distillation columns sequences of Dew pointing unit in the second phase of South Pars Gas Refinery. In this unit, three columns are u...