S. Bottaro

Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data

The paper improves protein stability prediction by modifying existing models with a self-derived term, enhancing their performance without additional training or data.

Discovering functionally important sites in proteins

This paper introduces a machine learning method to predict functional sites in proteins by integrating sequence conservation and biophysical stability models, validated through experimental data on missense variants.

Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

This study predicts the 3D structures and dynamics of five RNA stem loops in the SARS-CoV-2 5' UTR using molecular dynamics simulations and enhanced sampling techniques.

Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

This study integrates NMR, SAXS, SANS, and molecular dynamics simulations to characterize the structure and dynamics of two nanodiscs, revealing conformational heterogeneity and lipid ordering differences.

Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop

The paper integrates NMR and simulations to study UUCG RNA stem-loop dynamics, identifying two states and showing MD simulations overestimate a non-native conformation.

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

The paper combines molecular dynamics simulations with small-angle scattering data to study multi-domain proteins, showing how refining simulations against SAXS data improves agreement with experiments.

Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach

This paper introduces a Bayesian/Maximum Entropy method to refine molecular simulations using experimental data, producing a conformational ensemble that matches experimental values while maximizing entropy.

Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

The paper determines the conformational ensemble of RNA tetranucleotides using NMR data and molecular dynamics simulations with a reweighting scheme.