Related papers: Ligand Discrimination in Myoglobin from Linear-Sca…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
Hydrogen bonding is an important non-covalent interaction that plays a major role in molecular self-organization and supramolecular structures. It can be described accurately with ab initio quantum chemical wave function methods, which…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
The vibrational frequency of hydrogen molecules has been observed to increase strongly with He concentration in helium hydrogen fluid mixtures. This has been associated with He-H interactions, either directly through chemical bonding, or…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
The phase behavior and kinetic pathways of Li1+xV3O8 are investigated by means of density functional theory (DFT) and a cluster expansion (CE) methodology that approximates the system Hamiltonian in order to identify the lowest energy…
The cornerstone of computational drug design is the calculation of binding affinity between two biological counterparts, especially a chemical compound, i.e., a ligand, and a protein. Predicting the strength of protein-ligand binding with…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
The dissociation of hydrogen molecules on the \gamma-U(100) surface is systematically studied with the density functional theory method. Through potential energy surface calculations, we find that hydrogen molecules can dissociate without…
We recently showed that the DFT+U approach with a linear-response U yields adiabatic energy differences biased towards high spin [Mariano et al. J. Chem. Theory Comput. 2020, 16, 6755-6762]. Such bias is removed here by employing a…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Hybrid systems, which take advantage of low material dimensionality, have great potential for designing nanoscale devices. Quantum dots (QDs) -- a 0D nanostructure -- can be combined with 2D monolayers to achieve success in photovoltaics…
We present an approach to the DFT+U method (Density Functional Theory + Hubbard model) within which the computational effort for calculation of ground state energies and forces scales linearly with system size. We employ a formulation of…
Magnesium (Mg) has mechanical properties similar to bone tissue, and Mg ions take part in the metabolism. This makes Mg of interest for biocompatible degradable body implants, provided that its high corrosion rate can be inhibited. Slightly…
Molecular interactions are key to many chemical and biological processes like protein function. In many signaling processes they occur in sub-cellular areas displaying nanoscale organizations and involving molecular assemblies. The…
Photoelectron Angular Distributions (PADs) resulting from 800 nm and 1300 nm strong field ionization of impulsively aligned CF$_3$I molecules were analyzed using time-dependent density functional theory (TDDFT). The normalized difference…
Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics…
The electrical, magnetic, thermal and optical characteristics of Gallium (Ga) doped silicene are investigated using density functional theory (DFT). The effect of doping is studied by tuning dopant concentrations as well as examining varied…