Related papers: Absolute FKBP binding affinities obtained via non-…
Measurement-based entanglement is a method for entangling quantum systems through the state projection that accompanies a parity measurement. We derive a stochastic master equation describing measurement-based entanglement of a pair of…
The simplest model for non-congruent phase transition of gas-liquid type was developed in frames of modified model with no associations of a binary ionic mixture (BIM) on a homogeneous compressible ideal background (or non-ideal) electron…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-$\beta$(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an…
We incorporate explicit, non-perturbative treatment of spin-orbit coupling into ab initio auxiliary-field quantum Monte Carlo (AFQMC) calculations. The approach allows a general computational framework for molecular and bulk systems in…
Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…
We study experimentally accessible lower bounds on entanglement measures based on entropic uncertainty relations. Experimentally quantifying entanglement is highly desired for applications of quantum simulation experiments to fundamental…
Quantum link models provide an alternative non-perturbative formulation of Abelian and non-Abelian lattice gauge theories. They are ideally suited for quantum simulation, for example, using ultracold atoms in an optical lattice. This holds…
The protein-ligand binding affinity (PLA) prediction goal is to predict whether or not the ligand could bind to a protein sequence. Recently, in PLA prediction, deep learning has received much attention. Two steps are involved in deep…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
Two-dimensional systems such as quantum spin liquids or fractional quantum Hall systems exhibit anyonic excitations that possess more general statistics than bosons or fermions. This exotic statistics makes it challenging to solve even a…
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…
Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
We generalize solid-state tight-binding techniques for the spectral analysis of large superconducting circuits. We find that tight-binding states can be better suited for approximating the low-energy excitations than charge-basis states, as…
It is well established that amyloid fibril solubility is protein specific, but how solubility depends on the interactions between the fibril building blocks is not clear. Here we use a simple protein model and perform Monte Carlo…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…