Search results for "Molecular Dynamic"

Atomistic MD simulation of proteins in complex solvents

2009

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening.

2015

In drug discovery the reliable prediction of binding free energies is of crucial importance. Methods that combine molecular mechanics force fields with continuum solvent models have become popular because of their high accuracy and relatively good computational efficiency. In this research we studied the performance of molecular mechanics generalized Born surface area (MM-GBSA), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and solvated interaction energy (SIE) both in their virtual screening efficiency and their ability to predict experimentally determined binding affinities for five different protein targets. The protein-ligand complexes were derived with two different app…

A magnetic look into the protecting layer of Au25 clusters

2016

The field of molecular metal clusters protected by organothiolates is experiencing a very rapid growth. So far, however, a clear understanding of the fine interactions between the cluster core and the capping monolayer has remained elusive, despite the importance of the latter in interfacing the former to the surrounding medium. Here, we describe a very sensitive methodology that enables comprehensive assessment of these interactions. Pulse electron nuclear double resonance (ENDOR) was employed to study the interaction of the unpaired electron with the protons of the alkanethiolate ligands in four structurally related paramagnetic Au25(SR)0 18 clusters (R ¼ ethyl, propyl, butyl, 2-methylpro…

Functional Extrapolations to Tame Unbound Anions in Density-Functional Theory Calculations

2019

Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densitie…

A dynamic multiple receptor conformations (MD-MRC) approach to enhance early enrichment in virtual screening. A case study on PPAR-alpha

2016

Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State

2012

ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …

Proteins in Amorphous Saccharides: Structural and Dynamical Insights on Bioprotection

2011

We report on experimental and simulative insights on saccharide-based bioprotection, obtained through the study of proteins embedded in amorphous saccharide matrices. The data presented come from a complementary set of techniques (FTIR, MD simulations and SAXS), which provides a description of the bioprotection mechanism from the atomistic to the macroscopic level. The results concur to draw a picture in which bioprotection by saccharides can be explained in terms of a tight anchorage of the protein surface to a stiff matrix, via extended hydrogen-bond networks, whose properties are defined by all its components, and are strongly dependent on the water content. In particular, they show how …

Computational Modeling of Geminate Recombination and Energy Relaxation of Nitric Oxide in Myoglobin under Constant Illumination,

2011

Computational studies of biomolecular screening and interactions

2015

Blends of Semiflexible Polymers: Interplay of Nematic Order and Phase Separation

2021

Mixtures of semiflexible polymers with a mismatch in either their persistence lengths or their contour lengths are studied by Density Functional Theory and Molecular Dynamics simulation. Considering lyotropic solutions under good solvent conditions, the mole fraction and pressure is systematically varied for several cases of bending stiffness κ (the normalized persistence length) and chain length N. For binary mixtures with different chain length (i.e., NA=16, NB=32 or 64) but the same stiffness, isotropic-nematic phase coexistence is studied. For mixtures with the same chain length (N=32) and large stiffness disparity (κB/κA=4.9 to 8), both isotropic-nematic and nematic-nematic unmixing oc…