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Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simu...

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the o...

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force f...

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related are...

The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and a...

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked lig...

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC,...

Compounds 5-7 were synthesized from 4-tetralones with o-iodoanilines by a radical nucleophilic substitution or SRN1 reaction, and were pharmacologically evaluated in order to establish their possible antagonistic action ...

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provid...

La aspirina (ácido acetilsalicílico) es uno de los medicamentos más viejos y difundidos del mundo. Son múltiples sus beneficios, pero recién en los últimos años se han comenzado a desentrañar los mecanismos molec...

Conocida como ácido ascórbico, la Vitamina C es una vitamina que interviene en múltiples procesos, tales como: formación de hormonas, neurotransmisores, carnitina, conversión del colesterol en ácidos biliares, incr...

An approach for electronic structure calculations is described that generalizes both the pseudopotential method and the linear augmented-plane-wave (LAPW) method in a natural way. The method allows high-quality first-pri...

Materias / palabras clave: molecular structure and dynamics, bioinformatics and systems biology, molecular medicine, biomacromolecules, enzymology, molecular biophysics; Science: Microbiology

Materias / palabras clave: molecular structure, folding and dynamics, biophysical and molecular biological methods; Science: Biology (General)