Publications by authors named "Benjamin Ries"

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Beyond Barriers, Big Crystallization Hurdles: Atropisomerism in Beyond Rule of Five Compounds Explored by Computational and NMR Studies.
Nikolaos Angelos Stamos, Benjamin Ries, Regina Schneider, Pavleta Tzvetkova, Florian Montel

Mol Pharm· June 2025

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Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations.
Alejandro Martínez León, Benjamin Ries, Jochen S Hub, Aniket Magarkar

J Cheminform· May 2025

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IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates.
Linde Schoenmaker, Daan A Jiskoot, Jenke Scheen, Evien Cheng, Vytautas Gapsys, Benjamin Ries

J Phys Chem B· March 2025

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Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations.
Benjamin Ries, Richard J Gowers, Hannah M Baumann, David W H Swenson, Michael M Henry

J Chem Inf Model· November 2024

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Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery.
Benjamin Ries, Irfan Alibay, Nithishwer Mouroug Anand, Philip C Biggin, Aniket Magarkar

J Chem Inf Model· July 2024

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Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations.
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry

J Chem Theory Comput· March 2024

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Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.
Candide Champion, René Gall, Benjamin Ries, Salomé R Rieder, Emilia P Barros

J Chem Inf Model· November 2023

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Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities.
Emilia P Barros, Benjamin Ries, Candide Champion, Salomé R Rieder, Sereina Riniker

J Chem Inf Model· March 2023

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Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff.
Salomé R Rieder, Benjamin Ries, Alžbeta Kubincová, Candide Champion, Emilia P Barros

J Chem Phys· September 2022

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Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules.
Salomé R Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emilia P Barros

J Chem Inf Model· June 2022

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Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS.
Salomé R Rieder, Benjamin Ries, Candide Champion, Emilia P Barros, Philippe H Hünenberger

Chimia (Aarau)· April 2022

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RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology.
Benjamin Ries, Salomé Rieder, Clemens Rhiner, Philippe H Hünenberger, Sereina Riniker

J Comput Aided Mol Des· March 2022

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Recent developments in multiscale free energy simulations.
Emilia P Barros, Benjamin Ries, Lennard Böselt, Candide Champion, Sereina Riniker

Curr Opin Struct Biol· February 2022

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Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure.
Benjamin Ries, Karl Normak, R Gregor Weiß, Salomé Rieder, Emília P Barros

J Comput Aided Mol Des· February 2022

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Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability.
Stephanie M Linker, Christian Schellhaas, Benjamin Ries, Hans-Jörg Roth, Marianne Fouché

RSC Adv· February 2022

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Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling.
Gerhard König, Benjamin Ries, Philippe H Hünenberger, Sereina Riniker

J Chem Theory Comput· September 2021

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Passing the Barrier - How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides.
Stephanie M Linker, Shuzhe Wang, Benjamin Ries, Thomas Stadelmann, Sereina Riniker

Chimia (Aarau)· June 2021

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A Perspective on Virtual Events during the Corona Pandemic Exemplified by the CareerTrack with IBM Research Europe - Zurich.
Benjamin Ries, Laura A Völker, Romain Dubey, Stephanie Linker

Chimia (Aarau)· June 2021

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Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties.
Christian Comeau, Benjamin Ries, Thomas Stadelmann, Jacob Tremblay, Sylvain Poulet

J Med Chem· May 2021

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Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations.
Benjamin Ries, Stephanie M Linker, David F Hahn, Gerhard König, Sereina Riniker

J Chem Inf Model· February 2021

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Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy.
R Gregor Weiß, Benjamin Ries, Shuzhe Wang, Sereina Riniker

J Chem Phys· February 2021

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Examining Emergency Department Treatment Processes in Severe Pediatric Traumatic Brain Injury.
Ali Ajdari, Linda Ng Boyle, Nithya Kannan, Ali Rowhani-Rahbar, Jin Wang, Benjamin Ries

J Healthc Qual· July 2018

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