Benjamin Ries

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 18

Top Topics

Molecular Dynamics Simulations

Density Functional Theory

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

The Journal of chemical physics

Journal of computer-aided molecular design

This page only lists publications with an associated author ORCID identifier.

Publications

Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James R B Eastwood, Richard J Gowers
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Journal of chemical theory and computation 20 (5) (2024)
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James R B Eastwood, Richard J Gowers
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Journal of chemical theory and computation (2024)
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James R B Eastwood, Richard J Gowers
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Journal of chemical theory and computation 20 (5) (2024)
Benjamin Ries, Irfan Alibay, Nithishwer Mouroug Anand, Philip Charles Biggin, Aniket Magarkar
Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery. Journal of chemical information and modeling 64 (14) (2024)
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James R B Eastwood, Richard J Gowers
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Journal of chemical theory and computation 20 (5) (2024)
Benjamin Ries, Irfan Alibay, Nithishwer Mouroug Anand, Philip Charles Biggin, Aniket Magarkar
Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery. Journal of chemical information and modeling (2024)
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James R B Eastwood, Richard J Gowers
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Journal of chemical theory and computation 20 (5) (2024)
Candide Champion, René Gall, Benjamin Ries, Salomé R Rieder, Emilia P Barros, Sereina Riniker
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. Journal of chemical information and modeling (2023)
Emilia P Barros, Benjamin Ries, Candide Champion, Salomé R Rieder, Sereina Riniker
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. Journal of chemical information and modeling (2023)
Salomé R Rieder, Benjamin Ries, Alžbeta Kubincová, Candide Champion, Emilia P Barros, Philippe H Hünenberger, Sereina Riniker
Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff. The Journal of chemical physics 157 (10) (2022)
Salomé R Rieder, Benjamin Ries, Candide Champion, Emilia P Barros, Philippe H Hünenberger, Sereina Riniker
Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS. Chimia 76 (4) (2022)
Benjamin Ries, Karl Normak, R Gregor Weiß, Salomé R Rieder, Emilia P Barros, Candide Champion, Gerhard König, Sereina Riniker
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. Journal of computer-aided molecular design 36 (2) (2022)
Stephanie M Linker, Christian Schellhaas, Benjamin Ries, Hans-Jörg Roth, Marianne Fouché, Stephane Rodde, Sereina Riniker
Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability. RSC advances 12 (10) (2022)
Salomé R Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emilia P Barros, Philippe H Hünenberger, Sereina Riniker
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. Journal of chemical information and modeling 62 (12) (2022)
Benjamin Ries, Salomé R Rieder, Clemens Rhiner, Philippe H Hünenberger, Sereina Riniker
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. Journal of computer-aided molecular design 36 (3) (2022)
Gerhard König, Benjamin Ries, Philippe H Hünenberger, Sereina Riniker
Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling. Journal of chemical theory and computation 17 (9) (2021)
Christian Comeau, Benjamin Ries, Thomas Stadelmann, Jacob Tremblay, Sylvain Poulet, Ulrike Fröhlich, Jérôme Côté, Pierre-Luc Boudreault, Rabeb Mouna Derbali, Philippe Sarret, Michel Grandbois, Grégoire Leclair, Sereina Riniker, Eric Marsault
Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties. Journal of medicinal chemistry 64 (9) (2021)
R Gregor Weiß, Benjamin Ries, Shuzhe Wang, Sereina Riniker
Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy. The Journal of chemical physics 154 (8) (2021)