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Biomolecular Simulation: a Perspective from High Performance Computing

Publications associées (40)

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We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the reti ...

2014

Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalentl ...

Amer Chemical Soc2013

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Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of ...

Amer Chemical Soc2013

Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case

Fabio Trani

An integrated computational approach built on quantum mechanical (QM) methods, purposely tailored inter-and intra-molecular force fields and continuum solvent models combined with time-independent and timedependent schemes to account for nuclear motion eff ...

2012

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We investigated the cathodic and anodic limits of six room-temperature ionic liquids (ILs) formed from a combination of two common cations, 1-butyl-3-methylimidazolium (BMIM) and N,N-propylmethylpyrrolidinium (P13), and three common anions, PF6, BF4, and b ...

2011

The solvent shell structure of aqueous iodide: X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations

Majed Chergui, Ivano Tavernelli, Van Thai Pham, Renske Marjan van der Veen

The L-3 X-ray absorption spectrum of aqueous iodide is reported, and its EXAFS is compared to theoretical spectra reconstructed from the radial distribution function of the iodide hydration obtained from classical, hybrid Quantum Mechanics Molecular Mechan ...

Elsevier2010

Improved United-Atom Force Field for 1-Alkyl-3-methylimidazolium Chloride

Berend Smit, Ting Chen

We have developed a united atom (UA) nonpolarizable force field for 1-alkyl-3-methyl-imidazolium chloride ([Cnmim][Cl], n = 1, 2, 4, 6, 8), a potential solvent for the pretreatment of lignocellulosic biomass. The charges were assigned by fitting the electr ...

2010

Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study

Ursula Röthlisberger, Michele Cascella

Recently, Hasserodt et al. proposed new HIV-1 drug candidates based on a weak N center dot center dot center dot CO interaction, designed to be a close transition state analog (Gautier et al. Bioorg. Med. Chem. 2006, 14, 3835-3847; Waibel et al. J. Bioorg. ...

2010

Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Ursula Röthlisberger, Denis Bucher, Leonardo Guidoni

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...

2009