Michael Schauperl
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View article: A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics Open
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenien…
View article: A fast, convenient, polarizable electrostatic model for molecular dynamics
A fast, convenient, polarizable electrostatic model for molecular dynamics Open
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered, polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenie…
View article: A fast, convenient, polarizable electrostatic model for molecular dynamics
A fast, convenient, polarizable electrostatic model for molecular dynamics Open
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered, polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenie…
View article: A fast, convenient, polarizable electrostatic model for molecular dynamics
A fast, convenient, polarizable electrostatic model for molecular dynamics Open
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered, polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenie…
View article: A fast, convenient, polarizable electrostatic model for molecular dynamics
A fast, convenient, polarizable electrostatic model for molecular dynamics Open
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered, polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenie…
View article: Recent applications of computational methods to allosteric drug discovery
Recent applications of computational methods to allosteric drug discovery Open
Interest in exploiting allosteric sites for the development of new therapeutics has grown considerably over the last two decades. The chief driving force behind the interest in allostery for drug discovery stems from the fact that in compa…
View article: Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning
Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning Open
Stacking interactions play a crucial role in drug design, as we can find aromatic cores or scaffolds in almost any available small molecule drug. To predict optimal binding geometries and enhance stacking interactions, usually high-level q…
View article: Quantum Chemical Microsolvation by Automated Water Placement
Quantum Chemical Microsolvation by Automated Water Placement Open
We developed a quantitative approach to quantum chemical microsolvation. Key in our methodology is the automatic placement of individual solvent molecules based on the free energy solvation thermodynamics derived from molecular dynamics (M…
View article: Data-driven analysis of the number of Lennard–Jones types needed in a force field
Data-driven analysis of the number of Lennard–Jones types needed in a force field Open
Force fields used in molecular simulations contain numerical parameters, such as Lennard–Jones (LJ) parameters, which are assigned to the atoms in a molecule based on a classification of their chemical environments. The number of classes, …
View article: Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds
Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds Open
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry (ITC) and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exot…
View article: Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds
Experimental Characterization of the Association of Nine Novel Cyclodextrin Derivatives with Two Guest Compounds Open
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry (ITC) and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exot…
View article: Solvation Thermodynamics in Different Solvents: Water–Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory
Solvation Thermodynamics in Different Solvents: Water–Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory Open
Reliable information on partition coefficients plays a key role in drug development, as solubility decisively affects bioavailability. In a physicochemical context, the partition coefficient of a solute between two different solvents can b…
View article: Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments
Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments Open
The relation of surface polarity and conformational preferences is decisive for cell permeability and thus bioavailability of macrocyclic drugs. Here, we employ grid inhomogeneous solvation theory (GIST) to calculate solvation free energie…
View article: Data-driven analysis of the number of Lennard-Jones types needed in a force field
Data-driven analysis of the number of Lennard-Jones types needed in a force field Open
We optimized force fields with smaller and larger sets of chemically motivated Lennard-Jones types against the experimental properties of organic liquids. Surprisingly, we obtained results as good as or better than those from much more com…
View article: Data-driven analysis of the number of Lennard-Jones types needed in a force field
Data-driven analysis of the number of Lennard-Jones types needed in a force field Open
We optimized force fields with smaller and larger sets of chemically motivated Lennard-Jones types against the experimental properties of organic liquids. Surprisingly, we obtained results as good as or better than those from much more com…
View article: Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)
Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2) Open
The restrained electrostatic potential (RESP) approach is a highly regarded and widely used method of assigning partial charges to molecules for simulations. RESP uses a quantum-mechanical method that yields fortuitous overpolarization and…
View article: STACKED – <u>S</u>olvation <u>T</u>heory of <u>A</u>romatic <u>C</u>omplexes as <u>K</u>ey for <u>E</u>stimating <u>D</u>rug Binding
STACKED – Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding Open
The use of fragments to biophysically characterize a protein binding pocket and determine the strengths of certain interactions is a computationally and experimentally commonly applied approach. Almost all drug like molecules contain at le…
View article: Hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> GIVA predict its membrane-associated parts and its highly hydrated binding site
Hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> GIVA predict its membrane-associated parts and its highly hydrated binding site Open
During biological events, the water molecules associated with the protein are re-oriented to adapt to the new conditions, inducing changes in the system's free energy. The characterization of water structure and thermodynamics may facilita…
View article: Performance of DFT functionals for properties of small molecules containing beryllium, tungsten and hydrogen
Performance of DFT functionals for properties of small molecules containing beryllium, tungsten and hydrogen Open
A comparative study of bond lengths, atomization energies and vibrational frequencies for a set of neutral molecules Ben, BenHm, Wn, WnBem, and WnHm with m + n ≤ 4 in their ground state is presented. We compare 16 density functionals chose…
View article: Hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> GIVA predict its membrane-associated parts and its highly hydrated binding site
Hydration thermodynamics of cytosolic phospholipase A<sub>2</sub> GIVA predict its membrane-associated parts and its highly hydrated binding site Open
During biological events, the water molecules associated with the protein are re-oriented to adapt to the new conditions, inducing changes in the system’s free energy. The characterization of water structure and thermodynamics may facilita…
View article: Raw ITC and NOESY data for the SAMPL7 Cyclodextrin Derivatives Challenge
Raw ITC and NOESY data for the SAMPL7 Cyclodextrin Derivatives Challenge Open
This provides the raw ITC and NOESY datasets associated with the SAMPL7 modified cyclodextrin binding challenge (focusing on host-guest binding), as described at: https://github.com/samplchallenges/SAMPL7/tree/master/host_guest/cyclodextri…
View article: Raw ITC and NOESY data for the SAMPL7 Cyclodextrin Derivatives Challenge
Raw ITC and NOESY data for the SAMPL7 Cyclodextrin Derivatives Challenge Open
This provides the raw ITC and NOESY datasets associated with the SAMPL7 modified cyclodextrin binding challenge (focusing on host-guest binding), as described at: https://github.com/samplchallenges/SAMPL7/tree/master/host_guest/cyclodextri…
View article: Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models Open
The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popu…
View article: Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models Open
The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popu…
View article: Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2)
Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2) Open
Many molecular simulation force fields represent the charge distributions of molecules with atom-centered partial charges, so simulations with these force fields require that partial charges be assigned to the molecules of interest. The re…
View article: Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2)
Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2) Open
Many molecular simulation force fields represent the charge distributions of molecules with atom-centered partial charges, so simulations with these force fields require that partial charges be assigned to the molecules of interest. The re…
View article: Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models Open
The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popu…
View article: Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models Open
The accuracy of classical molecular mechanics (MM) force fields used for condensed phase molecular simulations depends strongly on the accuracy of modeling nonbonded interactions between atoms, such as electrostatic interactions. Some popu…
View article: Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces
Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces Open
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high inte…