Binding phosphatidylinositol 4,5-bisphosphate (PIP2) is essential for Kir2.1(encoded by KCNJ2), function. Disease associated KCNJ2 mutations, such as those with Andersen-Tawil Syndrome (ATS), may exert molecular dysfunction interrupting PIP2 binding, however a full-length model of Kir2.1 has not been developed to explore this hypothesis. Elucidate the structure and determine functional impact c...

A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool t...

Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GR...

It has come to the authors’ attention recently that a similar approach for embedding proteins into equilibrated lipid bilayers described in J. Comp. Chem. 31, 2169 (2010) had been proposed prior to their work by Dr. Semen Yesylevskyy in J. Chem. Inf. Mod. 47 1986 (2007) and implemented as a ProtSqueeze tool, which the authors have unfortunately overlooked. Although the focus of the above paper ...

We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4...

The properties of sodium dodecyl sulfate (SDS) aggregates were studied through extensive molecular dynamics simulations with explicit solvent. First, we provide a parametrization of the model within Gromacs. Then, we probe the kinetics of aggregation by starting from a random solution of SDS molecules and letting the system explore its kinetic pathway during the aggregation of multiple units. W...

microtubules, the active filaments with tubular shapes, play important roles in a wide range of cellular functions, including structural supports, mitosis, cytokinesis, and vesicular transport, which are essential for the growth and division of eukaryotic cells. finding properties of microtubules is one of the main concerns of scientists. this work helps to obtain mechanical properties of micro...

in hard disk drives (hdd), it is necessary to decrease the flying height (fh) between the head and the disk (currently, fh is around 3-5 nm) so as to increase recording densities. retaining the solid lubricant has become a difficult proposition owing to intermittent contact between the surfaces. ztmd and z are used as solid lubricant to lubricate these interfaces. in this paper, the behavior of...

Lipid formulations can improve the bioavailability of drugs that have low aqueous solubility. A variety of chemical compounds, including triglyceride oils (lipids), fatty acid esters and surfactants, can be included in lipid formulations. This heterogeneity makes spectroscopic study of the in ternal structure of formulation difficult. Understanding of lipid formulations at a molecular level wil...

The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to microseconds time scales or faster can be studied directly. Unfortunately, apart from a few exceptions, relevant processes, such as chemical reactions or many large scale conformational transitions in proteins, occur at slo...