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Computational modeling of protein-protein interactions (PPIs) is a high priority because it is essential for understanding nearly all cellular functions and for addressing the limitations of time-consuming experimental m...

La integración entre biotecnología y nanotecnología conforma la bionanotecnología que es una disciplina que permite potenciar la utilización de biomoléculas con materiales abióticos de diseño a escala nanométric...

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...

Previous article Next article Fractional Brownian Motions, Fractional Noises and ApplicationsBenoit B. Mandelbrot and John W. Van NessBenoit B. Mandelbrot and John W. Van Nesshttps://doi.org/10.1137/1010093PDFBibTexSecti...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

Subjects / keywords: supramolecular and nanoscale chemistry, computational and modeling chemistry, crystallography and physical methods, molecular chemistry, medicinal and bioinorganic chemistry, catalysis and organometallic chemistry; Scien...

The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingre...

This work reexamines the effect of the exchange screening parameter omega on the performance of the Heyd-Scuseria-Ernzerhof (HSE) screened hybrid functional. We show that variation of the screening parameter influences s...

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (b...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The va...

We describe a graphical system for automatically generating multiple 2D diagrams of ligand-protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond interaction patterns and hydrophobic contacts be...

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 pr...