Dataset - B2FIND

Movies of thin film water on NaCl(100) surface

Videos showing water molecules at a sodium chloride (NaCl) solid surface for different water content. The force field for the water is TIP4P/epsilon...

Additional data related to Schnee et al.: Mechanistic basis of the increased ...

This data collection contains additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase...

Python scripts related to MD simulations in "Preferential interaction of DNMT...

Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant...

Material for the paper "The possible role of lipid bilayer properties in the ...

Simulation input scripts to produce the data presented in the manuscript "The possible role of lipid bilayer properties in the evolutionary disappearance of betaine lipids in...

Supplementary material for 'An atomistic view on the uptake of aromatic compo...

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for all...

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Prot...

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' containing files to (re-)execute GROMACS simulations performed during the...

Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs o...

Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the...

Supplementary material for 'Umbrella sampling and double decoupling data for ...

This dataset contains all relevant simulation input files (topologies, coordinates, simulation parameters), generated simulation output (final configurations, time series of...

Supplementary material for 'Confinement Effects for Efficient Macrocyclizatio...

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory Mdp) are...

MD simulations and ML dataset of HLA-EpiCheck epitope predictor tool

This dataset contains all the data used to implement the B-cell epitope predictor tool called HLA-EpiCheck (see https://doi.org/10.1101/2023.12.18.572133). CONTENTS: -...

Molecular dynamics data for UDG-dsDNA

UDG-dsDNA-MD simulation. Initially, the UDG-dsDNA complex was solvated using the TIP3P water model, and 0.15 M sodium and chloride ions were added to neutralize the system....

Molecular dynamics data for UDG enzyme

UDG enzyme-MD simulation. Initially, the UDG enzyme was solvated using the TIP3P water model, and 0.15 M sodium and chloride ions were added to neutralize the system. Before...

Molecular dynamics data for DNA base flipping

DNA base flipping trajectory files. Initial state is a double stranded DNA containing a thymine mutated to a uracil. Uracil is then flipped out according to a 100ns simulation....