Histone deacetylation in epigenetics: an attractive target for anticancer therapy
The reversible histone acetylation and deacetylation are epigenetic phenomena that play
critical roles in the modulation of chromatin topology and the regulation of gene expression …
critical roles in the modulation of chromatin topology and the regulation of gene expression …
Design, parameterization, and implementation of atomic force fields for adsorption in nanoporous materials
Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
We present the derivation of a new molecular mechanical force field for simulating the
structures, conformational energies, and interaction energies of proteins, nucleic acids, and …
structures, conformational energies, and interaction energies of proteins, nucleic acids, and …
On the inner workings of Monte Carlo codes
D Dubbeldam, A Torres-Knoop, KS Walton - Molecular Simulation, 2013 - Taylor & Francis
We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the …
DA Pearlman, DA Case, JW Caldwell, WS Ross… - Computer Physics …, 1995 - Elsevier
We describe the development, current features, and some directions for future development
of the AMBER package of computer programs. This package has evolved from a program …
of the AMBER package of computer programs. This package has evolved from a program …
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
WD Cornell, P Cieplak, CI Bayly… - Journal of the American …, 2002 - ACS Publications
We apply a new restrained electrostatic potential fit charge model (two-stage RESP) to
conformational analysis and the calculation of intermolecular interactions. Specifically, we …
conformational analysis and the calculation of intermolecular interactions. Specifically, we …
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
I Massova, PA Kollman - Perspectives in drug discovery and design, 2000 - Springer
Significant progress has been achieved in computational methods to treat solvent effects in
recent years. Among various techniques, the continuum solvent approach appears to be …
recent years. Among various techniques, the continuum solvent approach appears to be …
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
P Cieplak, WD Cornell, C Bayly… - Journal of …, 1995 - Wiley Online Library
We present the derivation of charges of ribo-and deoxynucleosides, nucleotides, and
peptide fragments using electrostatic potentials obtained from ab initio calculations with the …
peptide fragments using electrostatic potentials obtained from ab initio calculations with the …
[HTML][HTML] Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator: coactivator interactions
I Radhakrishnan, GC Pérez-Alvarado, D Parker… - Cell, 1997 - cell.com
The nuclear factor CREB activates transcription of target genes in part through direct
interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent …
interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent …
[HTML][HTML] A novel mode of DNA recognition by a β‐sheet revealed by the solution structure of the GCC‐box binding domain in complex with DNA
The 3D solution structure of the GCC‐box binding domain of a protein from Arabidopsis
thaliana in complex with its target DNA fragment has been determined by heteronuclear …
thaliana in complex with its target DNA fragment has been determined by heteronuclear …