Andreas F. Tillack
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View article: Meeko: molecule parameterization and software interoperability for docking and beyond
Meeko: molecule parameterization and software interoperability for docking and beyond Open
Molecule parametrization is an essential requirement to guarantee the accuracy of simulations. Parametrization includes a proper perception of chemical properties such as bonds, formal charges and protonation states. This includes large bi…
View article: Microbiota-derived secondary bile acids promote STING activation and antitumor activity
Microbiota-derived secondary bile acids promote STING activation and antitumor activity Open
Microbiota metabolism generates diverse bile acids that are associated with health and disease, but the molecular targets and mechanisms of action for these metabolites have not been fully elucidated. Using bile acid photoaffinity probes a…
View article: Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance
Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance Open
Recent advances in structural biology have led to the publication of a wealth of high‐resolution x‐ray crystallography (XRC) and cryo‐EM macromolecule structures, including many complexes with small molecules of interest for drug design. W…
View article: Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance
Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance Open
Recent advances in structural biology have led to the publica- tion of a wealth of high resolution x-ray crystallography and cryo-EM macromolecule structures, including many complexes with small molecules of interest for drug design. While…
View article: Multi-scale theory-assisted nano-engineering of plasmonic-organic hybrid electro-optic device performance
Multi-scale theory-assisted nano-engineering of plasmonic-organic hybrid electro-optic device performance Open
Multi-scale (correlated quantum and statistical mechanics) modeling methods have been advanced and employed to guide the improvement of organic electro-optic (OEO) materials, including by analyzing electric field poling induced electro-opt…
View article: Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species Open
We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in a number of applications alre…
View article: Reactive Docking: a computational method for high-throughput virtual screenings of reactive species
Reactive Docking: a computational method for high-throughput virtual screenings of reactive species Open
We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in a number of applications alre…
View article: Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results
Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results Open
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries in early stage drug discovery. As the size of compound libraries which can feasibly be screened grows, so do the challe…
View article: Ringtail: a Python tool for efficient management and storage of virtual screening results
Ringtail: a Python tool for efficient management and storage of virtual screening results Open
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large …
View article: Performance evaluation of flexible macrocycle docking in AutoDock
Performance evaluation of flexible macrocycle docking in AutoDock Open
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular…
View article: Recommendation: Performance evaluation of flexible macrocycle docking in AutoDock — R0/PR3
Recommendation: Performance evaluation of flexible macrocycle docking in AutoDock — R0/PR3 Open
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular…
View article: Performance evaluation of flexible macrocycle docking in AutoDock
Performance evaluation of flexible macrocycle docking in AutoDock Open
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular…
View article: AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings Open
AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or…
View article: AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings Open
AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other docking engines in the AutoDock Suite, it lacks features that support modeling of specific systems such as macrocycle…
View article: AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings Open
AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other docking engines in the AutoDock Suite, it lacks features that support modeling of specific systems such as macrocycle…
View article: High-throughput virtual laboratory for drug discovery using massive datasets
High-throughput virtual laboratory for drug discovery using massive datasets Open
Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit su…
View article: Accelerating A <scp>uto</scp> D <scp>ock</scp> 4 with GPUs and Gradient-Based Local Search
Accelerating A <span>uto</span> D <span>ock</span> 4 with GPUs and Gradient-Based Local Search Open
AutoDock4 is a widely used program for docking small molecules to macromolecular targets. It describes ligand-receptor interactions using a physics-inspired scoring function that has been proven useful in a variety of drug discovery projec…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protei…
View article: GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer Open
Protein-ligand docking is an in silico tool used to screen potential drug\ncompounds for their ability to bind to a given protein receptor within a\ndrug-discovery campaign. Experimental drug screening is expensive and time\nconsuming, and…
View article: Test set of 140 complexes for AutoDock-GPU
Test set of 140 complexes for AutoDock-GPU Open
Set of 140 protein-ligand complexes =================================== # Overview The ligands herein vary in the number of atoms and number of rotatable bonds. This is the full data set used in the following study: Accelerating AutoDock…
View article: Test set of 140 complexes for AutoDock-GPU
Test set of 140 complexes for AutoDock-GPU Open
Set of 140 protein-ligand complexes =================================== # Overview The ligands herein vary in the number of atoms and number of rotatable bonds. This is the full data set used in the following study: Accelerating AutoDock…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of t…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of t…
View article: GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research Open
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it…
View article: Pre-exascale accelerated application development: The ORNL Summit experience
Pre-exascale accelerated application development: The ORNL Summit experience Open
High-performance computing (HPC) increasingly relies on heterogeneous architectures to achieve higher performance. In the Oak Ridge Leadership Facility (OLCF), Oak Ridge, TN, USA, this trend continues as its latest supercomputer, Summit, e…
View article: Hybrid electro-optics and chipscale integration of electronics and photonics
Hybrid electro-optics and chipscale integration of electronics and photonics Open
Taken together, theory-guided nano-engineering of organic electro-optic materials and hybrid device architectures have permitted dramatic improvement of the performance of electro-optic devices. For example, the voltage-length product has …
View article: Unraveling Excitonic Effects for the First Hyperpolarizabilities of Chromophore Aggregates
Unraveling Excitonic Effects for the First Hyperpolarizabilities of Chromophore Aggregates Open
Excitonic interactions often significantly affect the optoelectronic properties of molecular materials. However, their role in determining the nonlinear optical response of organic electro-optic materials remains poorly understood. In this…
View article: Shape matters: The case for Ellipsoids and Ellipsoidal Water
Shape matters: The case for Ellipsoids and Ellipsoidal Water Open
We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in our Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressio…