Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring...

UNLABELLED birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in pa...

Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters for main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameter...

MptpB is an essential secreted virulence factor for M. tuberculosis. Inhibition of MptpB impairs mycobacterial survival in host macrophages and thus helps reduce tuberculosis infections. However, the binding mode of the biphenyl inhibitors, which are known as some of the most potent MptpB inhibitors, remains unclear. In this study, to understand the interactions between biphenyl inhibitors and ...

Carbon nanotubes (CNT) allow easy entrance and passage of water [1] and are thus of interest for microfluidics. In electro-osmosis, charged double layers are set into motion by external electric fields. In recent simulations, electro-osmosis of water inside a CNT in the absence of free charges was observed and rationalized by invoking an electric-field-driven torque-vorticity conversion at orie...

In the hierarchical model of RNA folding, the flexibility of the junction regions is the dominant influence on the conformational ensemble of the helices, which are treated as as collection of rigid bodies. To account for this in our modeling, we created multiscale representations of the dPEG and sPEG constructs by coarse-graining the helices while retaining atomistic detail in the junction reg...

BACKGROUND AND THE PURPOSE OF THE STUDY The interactions between HIV-1 gp120 and mutated CD4 proteins were investigated in order to identify a lead structure for therapy based on competitive blocking of the HIV binding receptor for human T-cells. Crystal structures of HIV gp120-CD4 complexes reveal a close interaction of the virus receptor with CD4 Phe43, which is embedded in a pocket of the vi...