Author

S. Bottaro

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6

Signature Assays, Organisms & Methods

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Assay:structural biology· 4 Approach:deep learning· 2 Approach:mechanistic / dynamical model· 2 Research Focus:protein folding & dynamics· 2 Research Focus:protein structure prediction· 2 Approach:statistical model· 2 Approach:experimental assay· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

K. Lindorff-Larsen· 6 shared G. Bussi· 2 shared L. Arleth· 2 shared A. H. Larsen· 1 shared A. Stein· 1 shared B. Schiott· 1 shared B. Vogeli· 1 shared D. H. Turner· 1 shared

Activity by Year

2017-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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6 shared papersBiophysics

K. Lindorff-Larsen

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Author profile →

6 papers

Recent·Most cited

Discovering functionally important sites in proteins

M. Cagiada, S. Bottaro, S. Lindemose, S. M. Schenstrom, A. Stein, R. Hartmann-Petersen, K. Lindorff-Larsen

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.

bioRxiv · Jul 14, 2022Biophysics

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

S. Bottaro, G. Bussi, K. Lindorff-Larsen

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.

bioRxiv · Dec 11, 2020Biophysics

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

T. Bengtsen, V. L. Holm, L. R. Kjolbye, S. R. Midtgaard, N. T. Johansen, G. Tesei, S. Bottaro, B. Schiott, L. Arleth, K. Lindorff-Larsen

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.

bioRxiv · Jun 23, 2020Biophysics

Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop

S. Bottaro, P. J. Nichols, B. Vogeli, M. Parrinello, K. Lindorff-Larsen

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.

bioRxiv · Jan 4, 2020Biophysics

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

A. H. Larsen, Y. Wang, S. Bottaro, S. Grudinin, L. Arleth, K. Lindorff-Larsen

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.

bioRxiv · Dec 26, 2019Biophysics

Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations

S. Bottaro, G. Bussi, S. D. Kennedy, D. H. Turner, K. Lindorff-Larsen

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

bioRxiv · Dec 7, 2017Biophysics