Related papers: Absolute FKBP binding affinities obtained via non-…

We describe a non-parametric approach for accurate determination of the slowest relaxation eigenvectors of molecular dynamics. The approach is blind as it uses no system specific information. In particular, it does not require a functional…

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…

Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the…

The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…

The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting cells against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into…

The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand between the receptor…

An accurate prediction of protein-nucleic acid binding affinity is vital for deciphering genomic processes, yet existing approaches often struggle in reconciling high accuracy with interpretability and computational efficiency. In this…

One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…

The past years have witnessed impressive advances in electronic structure calculation, especially in the complexity and size of the systems studied, as well as in computation time. Linear scaling methods based on empirical tight-binding…

The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data…

We propose new summary measures of diagnostic test accuracy which can be used as companions to existing diagnostic accuracy measures. Conceptually, our summary measures are tantamount to the so-called Hellinger affinity and we show that…

Conformal field theories in curved backgrounds have been used to describe inhomogeneous one-dimensional systems, such as quantum gases in trapping potentials and non-equilibrium spin chains. This approach provided, in a elegant and simple…

Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…

The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…

In biology, there are several processes in which unfolded protein chains are transported along narrow-tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However,…

In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work focuses on blind flexible selfdocking, where we aim to predict the positions, orientations and…

Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…

We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…

Accurate measurements of kinetic rate constants for interacting biomolecules is crucial for understanding the mechanisms underlying intracellular signalling pathways. The magnitude of binding rates plays a very important molecular…

Fidelity is a fundamental measure for the closeness of two quantum states, which is important both from a theoretical and a practical point of view. Yet, in general, it is difficult to give good estimates of fidelity, especially when one…