Related papers: Binding Free Energies without Alchemy

Core-electron x-ray photoelectron spectroscopy is a powerful technique for studying the electronic structure and chemical composition of molecules, solids and surfaces. However, the interpretation of measured spectra and the assignment of…

Host-guest binding plays a crucial role in the functionality of various systems, and its efficiency is often quantified using the binding free energy, which represents the free-energy difference between the bound and dissociated states.…

Many models of interest in the natural and social sciences have no closed-form likelihood function, which means that they cannot be treated using the usual techniques of statistical inference. In the case where such models can be…

We prove the convergence of an adaptive mixed finite element method (AMFEM) for (nonsymmetric) convection-diffusion-reaction equations. The convergence result holds from the cases where convection or reaction is not present to convection-or…

This work undertakes to combine the interests of IsoGeometric Analysis (IGA) and standard Finite Element Methods (FEM) for the global/local simulation of structures. The idea is to adopt a hybrid global-IGA/local-FEM modeling, thereby…

Protein binder design has been transformed by hallucination-based methods that optimize structure prediction confidence metrics, such as the interface predicted TM-score (ipTM), via backpropagation. However, these metrics do not reflect the…

Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering…

This paper describes the development of the Four Model Tree Ensemble (FMTE). The FMTE is a composite of machine learning models trained on experimental binding energies from the Atomic Mass Evaluation (AME) 2012. The FMTE predicts binding…

Ligand-receptor interactions are fundamental to many biological processes. For example in antibody-based immunotherapies, the dynamics of an antibody binding with its target antigen directly influence the potency and efficacy of monoclonal…

Approximate Bayesian computation (ABC) is a popular likelihood-free inference method for models with intractable likelihood functions. As ABC methods usually rely on comparing summary statistics of observed and simulated data, the choice of…

A new method for calculating the total energy of Si systems is presented. The method is based on the effective-medium theory concept of a reference system. Instead of calculating the energy of an atom in the system of interest a reference…

Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…

We introduce a gradient-free framework for Bayesian Optimal Experimental Design (BOED) in sequential settings, aimed at complex systems where gradient information is unavailable. Our method combines Ensemble Kalman Inversion (EKI) for…

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…

We propose an adaptive iteratively linearized finite element method (AILFEM) in the context of strongly monotone nonlinear operators in Hilbert spaces. The approach combines adaptive mesh-refinement with an energy-contractive linearization…

ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…

Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…

The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable…

A recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and…

We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…