相关论文: On the Polarization of Ligands by Proteins

Correlated motions of proteins underpin many physiological mechanisms, such as substrate binding, signal transduction, enzymatic activity and allostery. These motions arise from low frequency collective movements of biomolecules and have…

Electrostatic interactions involving proteins depend not just on the ionic charges involved but also on their chemical identities. Here we examine the origins of incompletely understood differences in the strength of association of…

A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to…

Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…

In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…

Approximate molecular calculations via standard Kohn-Sham Density Functional Theory are exactly reproduced by performing self-consistent calculations on isolated fragments via Partition Density Functional Theory [Phys. Rev. A 82, 024501…

The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…

Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…

Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…

Quasi-optical experiments are emerging as a powerful technique to probe magnetic transitions in molecular spin systems. However, the simultaneous presence of the electric- and magnetic-dipole induced transitions poses the challenge of…

The molecular polarizability describes the tendency of a molecule to deform or polarize in response to an applied electric field. As such, this quantity governs key intra- and inter-molecular interactions such as induction and dispersion,…

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…

A systematic investigation of the nuclear-polarization effects in one- and few-electron heavy ions is presented. The nuclear-polarization corrections in the zeroth and first orders in $1/Z$ are evaluated to the binding energies, the…

Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…

The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site…

The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…

Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…

We present relativistic many-body calculations of total electron binding energy of neutral atoms up to element $Z=120$. Binding energy for ions may be found by subtracting known ionization potentials. Accuracy of the results for $17<Z…