Benjamin Ries
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View article: Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations
Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations Open
We present Moldrug, a computational tool for accelerating the hit-to-lead phase in structure-based drug design. Moldrug explores the chemical space using structural modifications suggested by the CReM library and by optimizing an adaptable…
View article: Beyond Barriers, Big Crystallization Hurdles: Atropisomerism in Beyond Rule of Five Compounds Explored by Computational and NMR Studies
Beyond Barriers, Big Crystallization Hurdles: Atropisomerism in Beyond Rule of Five Compounds Explored by Computational and NMR Studies Open
Stereochemical purity, stability, and selection of a suitable solid-state form are pivotal factors in pharmaceutical development, particularly for complex beyond Rule of 5 (bRo5) compounds. In this study, we explore the intricate interplay…
View article: IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates
IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates Open
Alchemical free energy calculations are becoming an increasingly prevalent tool in drug discovery efforts. Over the past decade, significant progress has been made in automating various aspects of this technique. However, one aspect hamper…
View article: Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations
Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations Open
We present Moldrug, a computational tool for accelerating the hit-to-lead phase in structure-based drug design. Moldrug explores the chemical space using structural modifications suggested by the CReM library and by optimizing an adaptable…
View article: Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations Open
Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python packag…
View article: Konnektor: A framework for using graph theory to plan networks for free energy calculations
Konnektor: A framework for using graph theory to plan networks for free energy calculations Open
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python pac…
View article: Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations Open
Relative binding free energy (RBFE) calculations have emerged as a powerful tool that supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular, the …
View article: Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases Open
Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine …
View article: Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations
Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations Open
Relative binding free energy (RBFE) calculations have emerged as a powerful tool supporting ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular the setu…
View article: Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases Open
Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine …
View article: Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases Open
Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine …
View article: Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities Open
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding …
View article: Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities Open
Macromolecular recognition and ligand binding are at the core of biological function and drug discovery efforts. Water molecules play a significant role in mediating the protein-ligand interaction, acting as more than just the surrounding …
View article: Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff
Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff Open
Replica-exchange enveloping distribution sampling (RE-EDS) is a pathway-independent multistate free-energy method currently implemented in the GROMOS software package for molecular dynamics (MD) simulations. It has a high intrinsic samplin…
View article: Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules Open
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's accep…
View article: Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS
Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS Open
Molecular dynamics (MD) simulations have become an important tool to investigate biological systems. Free-energy calculations based on MD are playing an increasingly important role for computer-aided drug design and material discovery in r…
View article: RE-EDS Using GAFF Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
RE-EDS Using GAFF Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules Open
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's accep…
View article: Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability
Polar/apolar interfaces modulate the conformational behavior of cyclic peptides with impact on their passive membrane permeability Open
This study uses molecular dynamics and Markov state models to analyse how interfaces interact with cyclic decapeptides and modulate their dynamic and equilibrium properties.
View article: Recent developments in multiscale free energy simulations
Recent developments in multiscale free energy simulations Open
Physics-based free energy simulations enable the rigorous calculation of properties, such as conformational equilibria, solvation or binding free energies. While historically most applications have occurred at the atomistic level of resolu…
View article: A Perspective on Virtual Events during the Corona Pandemic Exemplified by the CareerTrack with IBM Research Europe – Zurich
A Perspective on Virtual Events during the Corona Pandemic Exemplified by the CareerTrack with IBM Research Europe – Zurich Open
ISSN:0009-4293
View article: Passing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides
Passing the Barrier – How Computer Simulations Can Help to Understand and Improve the Passive Membrane Permeability of Cyclic Peptides Open
Proteins with large and flat binding sites as well as protein–protein interactions are considered ' undruggable ' with conventional small-molecule drugs. Cyclic peptides have been found to be capable of binding to such targets with high af…
View article: Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties
Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties Open
Incorporating small modifications to peptidic macrocycles can have a major influence on their properties. For instance, N-methylation has been shown to impact permeability. A better understanding of the relationship between permeability an…
View article: Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy
Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy Open
The combination of Markov state modeling (MSM) and molecular dynamics (MD) simulations has been shown in recent years to be a valuable approach to unravel the slow processes of molecular systems with increasing complexity. While the algori…
View article: Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy
Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy Open
The combination of Markov state modeling (MSM) and molecular dynamics (MD) simulations has been shown in recent years to be a valuable approach to unravel the slow processes of molecular systems with increasing complexity. While the algori…