نتایج جستجو برای: gromacs

تعداد نتایج: 302  

2017
Xiao-Nu Peng Jing Wang Wei Zhang

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...

Journal: :Bioinformatics 2011
Teong Han Chew Kwee Hong Joyce-Tan Farizuwana Akma Mohd Shahir Shamsir

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...

Journal: :The Journal of chemical physics 2013
Yoshitake Sakae Yuko Okamoto

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...

2014
Andrew T. Fenley Hari S. Muddana Michael K. Gilson

Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials ...

Journal: :Journal of molecular modeling 2012
Lihua Dong Junyou Shi Yongjun Liu

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 ...

Journal: :Physical review letters 2010
D J Bonthuis K Falk C N Kaplan D Horinek A N Berker L Bocquet R R Netz

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...

2017
Gurjant Singh Mahesh Kulharia

Bacterial biofilm is a protective, slippery and slimy coat secreted by bacterial cells. It helps in attaching to moisturized surfaces during colonization. Alginate is an important component as it is essential for retention of water and nutrients in biofilms. It is a polysaccharide consisting of β-D-mannuronic acid (M) and α-L-guluronic acid (G) monomers with 1-4 linkage. The alginate lyase (Alg...

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