Science
Furthermore, we create new software and hardware infrastructure for performing biomolecular simulations in high-throughput. Salient examples are ACEMD, HTMD or Metrocubo.
We would be happy to consider scientific collaborations with interested parties to demonstrate the potential of biomolecular simulations and deep learning. We are open to research projects (e.g. European projects) as well as other collaboration formats. Do not hesitate to contact us today.
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Publications
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
Journal of Chemical Information and Modeling
2023
NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics
arXiv preprint arXiv:2201.08110
2022
TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials
International Conference on Learning Representations
2022
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
arXiv preprint arXiv:2212.07492
2022
PlayMolecule glimpse: Understanding protein–ligand property predictions with interpretable neural networks
Journal of chemical information and modeling
2022
Structure based virtual screening: Fast and slow
Wiley Interdisciplinary Reviews: Computational Molecular Science
2022
TorchMD: A deep learning framework for molecular simulations
Journal of chemical theory and computation
2021
PlayMolecule CrypticScout: predicting protein cryptic sites using mixed-solvent molecular simulations
Journal of Chemical Information and Modeling
2020
SkeleDock: a web application for scaffold docking in PlayMolecule
Journal of Chemical Information and Modeling
2020
Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations
Scientific reports
2020
Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations
Journal of Chemical Information and Modeling
2020
AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations
J. Chem. Theory Comput.
2020
A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning
Journal of chemical information and modeling
2019
From target to drug: generative modeling for the multimodal structure-based ligand design
Molecular pharmaceutics
2019
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks
Bioinformatics
2019
DeltaDelta neural networks for lead optimization of small molecule potency
Chemical science
2019
Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots
Scientific Reports
2019
Shape-based generative modeling for de novo drug design
Journal of chemical information and modeling
2019
K deep: protein–ligand absolute binding affinity prediction via 3d-convolutional neural networks
Journal of chemical information and modeling
2018
Molecular-simulation-driven fragment screening for the discovery of new CXCL12 inhibitors
Journal of chemical information and modeling
2018
Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs
Scientific reports
2018
PlayMolecule BindScope: Large scale CNN-based virtual screening on the web
Bioinformatics
2018
PathwayMap: molecular pathway association with self-normalizing neural networks
Journal of chemical information and modeling
2018
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Nature chemistry
2017
High-throughput automated preparation and simulation of membrane proteins with HTMD
Journal of Chemical Theory and Computation
2017
DeepSite: protein-binding site predictor using 3D-convolutional neural networks
Bioinformatics
2017
Dimensionality reduction methods for molecular simulations
arXiv preprint arXiv:1710.10629
2017
PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations
Journal of chemical information and modeling
2017
Drug discovery and molecular dynamics: methods, applications and perspective beyond the second timescale
Current topics in medicinal chemistry
2017
The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor
Scientific reports
2016
HTMD: high-throughput molecular dynamics for molecular discovery
Journal of chemical theory and computation
2016
Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme
Scientific reports
2016
Binding kinetics in drug discovery
Molecular Informatics
2016
HTMD: A complete software workspace for simulation-guided drug design
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
2015
Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation
Molecular pharmacology
2015
AceCloud: molecular dynamics simulations in the cloud
Journal of Chemical Information and Modeling
2015
Insights from fragment hit binding assays by molecular simulations
Journal of chemical information and modeling
2015
Reranking docking poses using molecular simulations and approximate free energy methods
Journal of chemical information and modeling
2014
On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations
Journal of chemical theory and computation
2014
Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH
Biochemical Journal
2014
Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations
Journal of Chemical Information and Modeling
2014
Kinetic modulation of a disordered protein domain by phosphorylation
Nature communications
2014
Identification of slow molecular order parameters for Markov model construction
The Journal of chemical physics
2013
Visualizing the induced binding of SH2-phosphopeptide
Journal of chemical theory and computation
2012
Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase
Journal of the American Chemical Society
2012
High-throughput molecular dynamics: the powerful new tool for drug discovery
Drug discovery today
2012
Kinetic characterization of the critical step in HIV-1 protease maturation
Proceedings of the National Academy of Sciences
2012
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Proceedings of the National Academy of Sciences
2011
A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A
Journal of Chemical Theory and Computation
2011
Optimized potential of mean force calculations for standard binding free energies
Journal of Chemical Theory and Computation
2011
High-throughput all-atom molecular dynamics simulations using distributed computing
Journal of chemical information and modeling
2010
Induced effects of sodium ions on dopaminergic G-protein coupled receptors
PLoS Computational Biology
2010
Explicit solvent dynamics and energetics of HIV‐1 protease flap opening and closing
Proteins: Structure, Function, and Bioinformatics
2010
An implementation of the smooth particle mesh Ewald method on GPU hardware
Journal of Chemical Theory and Computation
2009
ACEMD: Accelerating biomolecular dynamics in the microsecond time scale
Journal of Chemical Theory and Computation
2009
The impact of accelerator processors for high-throughput molecular modeling and simulation
Drug discovery today
2008