Related papers: Fast tensor-based electrostatic energy calculation…
Recently the rank-structured tensor approach suggested a progress in the numerical treatment of the long-range electrostatic potentials in many-particle systems and the respective interaction energy and forces [39,40,2]. In this paper, we…
The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
In this paper, we propose and analyze the numerical algorithms for fast solution of periodic elliptic problems in random media in $\mathbb{R}^d$, $d=2,3$. We consider the stochastic realizations using checkerboard configuration of 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…
We present a fast and accurate method to calculate the electrostatic energy and forces of interacting particles with the boundary conditions appropriate to surfaces, i.e periodic in the two directions parallel to the surface and free in the…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…
We introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D $N\times N \times N$ grid with the computational requirements only \emph{weakly…
We study the computation of equilibrium points of electrostatic potentials: locations in space where the electrostatic force arising from a collection of charged particles vanishes. This is a novel scenario of optimization in which…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
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…
We calculate electrostatic potential landscapes for an external probe charge in the presence of a set of metallic islands. Our numerical calculation in three dimensions (3D)uses an efficient grid relaxation technique. The well-known…
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor…
Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with…
We introduce and analyze the new range-separated (RS) canonical/Tucker tensor format which aims for numerical modeling of the 3D long-range interaction potentials in multi-particle systems. The main idea of the RS tensor format is the…
In this paper, we apply the range-separated (RS) tensor format [6] for the construction of new regularization scheme for the Poisson-Boltzmann equation (PBE) describing the electrostatic potential in biomolecules. In our approach, we use…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
The binding of clusters of metal nanoparticles is partly electrostatic. We address difficulties in calculating the electrostatic energy when high charging energies limit the total charge to a single quantum, entailing unequal potentials on…
An efficient technique based on low-rank separated approximations is proposed for computation of three-dimensional integrals arising in the energy deposition model that describes ion-atomic collisions. Direct tensor-product quadrature…