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Physical Chemistry

Working Paper

Rapid interpretation of protein backbone rotation dynamics directly from spin relaxation data

Ricky Nencini, Efstathia Mantzari, Amanda Sandelin, Samuli Ollila

Version 1 posted 23 May 2024

149

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Physical Chemistry

Working Paper

QEBSS: Quality Evaluation Based Simulation Selection for analysis of conformational ensembles and dynamics of multidomain proteins

Amanda Sandelin, Ricky Nencini, Ekrem Yasar, Satoshi Fudo, Vassilis Stratoulias, Tommi Kajander, Samuli Ollila

Version 2 posted 17 March 2025

696

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Physical Chemistry

Working Paper

Probing the dynamic landscape of peptides in membrane mimics by synergized NMR experiments and MD simulations

Ricky Nencini, Morgan Regnier, Sofia Backlund, Efstathia Mantzari, Cory Dunn, Samuli Ollila

Version 1 posted 21 August 2023

222

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Theoretical and Computational Chemistry

Working Paper

Quantitative Comparison Against Experiments Reveals Imperfections in Force Fields' Descriptions of Phospholipid-Cholesterol Interactions

Matti Javanainen, Peter Heftberger, Jesper Madsen, Markus Miettinen, Georg Pabst, Samuli Ollila

Version 1 posted 15 June 2023

243

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Physical Chemistry

Working Paper

Charged small molecule binding to membranes in MD simulations evaluated against NMR experiments

Ricky Nencini, Samuli Ollila

Version 2 posted 01 August 2022

346

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Physical Chemistry

Review

Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks

Hanne S. Antila, Batuhan Kav, Markus S. Miettinen, Hector Martinez-Seara, Pavel Jungwirth, O. H. Samuli Ollila

Version 1 posted 22 March 2022

238

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Physical Chemistry

Working Paper

Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension

Carmelo Tempra, O.H. Samuli Ollila, Matti Javanainen

Version 1 posted 28 September 2021

422

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Theoretical and Computational Chemistry

Working Paper

Sharing Data from Molecular Simulations

Mark J. Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M.J.J. Bonvin, matthieu chavent, John Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E joseph jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel Smith, Phillip J. Stansfeld, Johanna Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov

Version 1 posted 09 September 2019

1,252

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Physical Chemistry

Working Paper

Overlay databank unlocks data-driven analyses of biomolecules for all

Anne Kiirikki, Hanne Antila, Lara Bort, Pavel Buslaev, Favela Fernando, Tiago Mendes Ferreira, Patrick Fuchs, Rebeca Garcia-Fandino, Ivan Gushchin, Batuhan Kav, Norbert Kučerka, Patrik Kula, Milla Kurki, Alexander Kuzmin, Anusha Lalitha, Fabio Lolicato, Jesper Madsen, Markus Miettinen, Cedric Mingham, Luca Monticelli, Ricky Nencini, Alexey Nesterenko, Thomas Piggot, Angel Pineiro, Nathalie Reuter, Suman Samantray, Fabian Suarez-Leston, Reza Talandashti, Samuli Ollila

Version 3 posted 05 December 2023

671

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Physical Chemistry

Working Paper

Conformational Rigidity Classification in Intrinsically Disordered Proteins via Integrated NMR and MD Simulations

Cajsa Malm, Mykhailo Girych, O. H. Samuli Ollila

Version 1 posted 18 April 2025

115

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Refine Search

10 results in Samuli Ollila in Authors: Samuli Ollila

Rapid interpretation of protein backbone rotation dynamics directly from spin relaxation data

QEBSS: Quality Evaluation Based Simulation Selection for analysis of conformational ensembles and dynamics of multidomain proteins

Probing the dynamic landscape of peptides in membrane mimics by synergized NMR experiments and MD simulations

Quantitative Comparison Against Experiments Reveals Imperfections in Force Fields' Descriptions of Phospholipid-Cholesterol Interactions

Charged small molecule binding to membranes in MD simulations evaluated against NMR experiments

Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks

Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension

Sharing Data from Molecular Simulations

Overlay databank unlocks data-driven analyses of biomolecules for all

Conformational Rigidity Classification in Intrinsically Disordered Proteins via Integrated NMR and MD Simulations

10 results in Authors: Samuli Ollila