Pascal T. Merz
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View article: Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters
Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters Open
Methods for calculating the relative binding free energy (RBFE) between ligands to a target protein are gaining importance in the structure-based drug discovery domain, especially as methodological advances and automation improve accuracy …
View article: alchemlyb: the simple alchemistry library
alchemlyb: the simple alchemistry library Open
alchemlyb is an open-source Python software package for the analysis of alchemical free energy calculations, an important method in computational chemistry and biology, most notably in the field of drug discovery (Merz et al., 2010). Its f…
View article: Combatting Climate Disinformation: Comparing the Effectiveness of Correction Placement and Type
Combatting Climate Disinformation: Comparing the Effectiveness of Correction Placement and Type Open
In this study, we investigated whether corrections can combat climate disinformation. Using a preregistered quota-based online experiment in Germany (N = 1401), we tested how the effectiveness of disinformation correction in reducing clima…
View article: No-go zone for Jews? Examining how news on anti-Semitic attacks increases victim blaming
No-go zone for Jews? Examining how news on anti-Semitic attacks increases victim blaming Open
Antisemitism is on the rise. Recently, discussions have considered so-called “no-go zones for Jews” (city areas Jews should avoid to reduce the likelihood of being attacked). In this context and drawing from attribution theory, we examined…
View article: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
Adding alchemical variables to metadynamics to enhance sampling in free energy calculations Open
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as pr…
View article: physical_validation: A Python package to assess the physical validity of molecular simulation results
physical_validation: A Python package to assess the physical validity of molecular simulation results Open
Molecular simulations such as molecular dynamics (MD) and Monte Carlo (MC) simulations are powerful tools allowing the prediction of experimental observables in the study of systems such as proteins, membranes, and polymeric materials. The…
View article: Testing for physical validity in molecular simulations
Testing for physical validity in molecular simulations Open
Advances in recent years have made molecular dynamics (MD) and Monte Carlo (MC) simulations powerful tools in molecular-level research, allowing the prediction of experimental observables in the study of systems such as proteins, membranes…
View article: Testing for Physical Validity in Molecular Simulations
Testing for Physical Validity in Molecular Simulations Open
Advances in recent years have made molecular dynamics (MD) and Monte Carlo (MC) simulations powerful tools in molecular-level research, allowing the prediction of experimental observables in the study of systems such as proteins, membranes…
View article: Testing for Physical Validity in Molecular Simulations
Testing for Physical Validity in Molecular Simulations Open
Advances in recent years have made molecular dynamics (MD) and Monte Carlo (MC) simulations powerful tools in molecular-level research, allowing the prediction of experimental observables in the study of systems such as proteins, membranes…
View article: Testing for Physical Validity in Molecular Simulations
Testing for Physical Validity in Molecular Simulations Open
Advances in recent years have made molecular dynamics (MD) and Monte Carlo (MC) simulations powerful tools in molecular-level research, allowing the prediction of experimental observables in the study of systems such as proteins, membranes…