Homology models of amidase-03 from Bacillus anthracis were constructed using Modeller (9v2). Modeller constructs protein models using an automated approach for comparative protein structure modeling by the satisfaction of spatial restraints. A template structure of Listeria monocytogenes bacteriophage PSA endolysin PlyPSA (PDB ID: 1XOV) was selected from protein databank (PDB) using BLASTp with...

Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of findi...

Molecular dynamics simulations with coarse-grained and/or simplified Hamiltonians are an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Structure-based Hamiltonians, simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics. SMOG@ctbp...

The increasing gap between plentiful computing elements and limited memory bandwidth makes it increasingly difficult and sometimes even infeasible for HPC community to port more applications onto many-core processor archi‐ tectures. The Sunway many-core processor SW26010 used to build the Sunway TaihuLight System contains a total of 260 heterogeneous cores. All these cores can be divided into 4...

Heterogeneous administrative domains, operating systems (OS), and libraries make it difficult for computational scientists to fully utilize metacomputers and grids. Dealing with the presence or absence of features on, say, different clusters, adds complexity. How can a user or high-performance computing (HPC) application abstract out the heterogeneity? One possible solution is to use a virtual ...

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...