نتایج جستجو برای: CHARMM
تعداد نتایج: 456 فیلتر نتایج به سال:
The distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics. Here, we describe melittin partitioning into dioleoylphosphatidylcholine lipids using CHARMM and OPLS force fields. Although the OPLS simulation failed to reproduce experimental results, the CHARMM s...
The similarity of the AMBER force field’s energy functional form with that of the CHARMM force field, gives the potential for direct translation of common bonding and nonbonding terms, along with their parameters, present in CHARMM topology and parameter files, with the intent of evaluation within the AMBER software; specifically the SANDER and PMEMD dynamics engines. To this extent, we have cr...
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores.
The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of he...
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the stu...
Breast cancer is one of the most common malignancies among women globally, posing a major public health burden. This study primly aimed to theoretically prove formation silver nanoparticles by Dimocarpus longan fruit phytoconstituents and targeted delivery phytoconstituent inside cavity HER2 protein. The algorithm adsorption location CHARMm-based docking were used find interaction between atoms...
The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinati...
The molecular dynamics code CHARMM is a popular research tool for computational biology. An increasing number of researchers are currently looking for affordable and adequate platforms to execute CHARMM or similar codes. To address this need, we analyze the resource requirements of a CHARMM molecular dynamics simulation on PC clusters with a particle mesh Ewald (PME) treatment of longrange elec...
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations ...
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