David Dotson
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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: Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields
Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields Open
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules i…
View article: Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields
Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields Open
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules i…
View article: SPICE 2.0.1
SPICE 2.0.1 Open
SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. It is…
View article: Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields
Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields Open
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules i…
View article: Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields
Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields Open
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules i…
View article: Tuning Potential Functions to Host–Guest Binding Data
Tuning Potential Functions to Host–Guest Binding Data Open
Software to more rapidly and accurately predict protein-ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of t…
View article: Tuning Potential Functions to Host–Guest Binding Data
Tuning Potential Functions to Host–Guest Binding Data Open
Software to more rapidly and accurately predict protein--ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of …
View article: Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors Open
We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncov…
View article: Tuning Potential Functions to Host–Guest Binding Data
Tuning Potential Functions to Host–Guest Binding Data Open
Software to more rapidly and accurately predict protein--ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of …
View article: Conditions at the interface between the space elevator tether and its climber
Conditions at the interface between the space elevator tether and its climber Open
A simple space elevator consists of a single tether extending well beyond geosynchronous altitude and a payload-carrying device which grips and climbs the tether. A friction-based, opposing wheel climber was judged most likely to be constr…
View article: Optical genome mapping identifies a novel pediatric embryonal tumor with a <i>ZNF532::NUTM1</i> fusion
Optical genome mapping identifies a novel pediatric embryonal tumor with a <i>ZNF532::NUTM1</i> fusion Open
The molecular characteristics of pediatric brain tumors have not only allowed for tumor subgrouping but have led to the introduction of novel treatment options for patients with specific tumor alterations. Therefore, an accurate histologic…
View article: Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field Open
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which gen…
View article: The Climber-Tether Interface of the Space Elevator
The Climber-Tether Interface of the Space Elevator Open
The conditions at the interface between the space elevator tether and its climber determine the requirements of the tether material and the climber design. Graphene super-laminate was found to have sufficient tensile strength to support th…
View article: Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field
Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field Open
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which gen…
View article: Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field Open
Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it …
View article: Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field Open
OpenFF Industry Public Dataset optimized at the (1) B3LYP-D3BJ / TDZP; (2) OpenFF-2.0.0; (3) Gaff-2.11-AM1BCC; (3) OPLS4 + default parameters; (4) OPLS4 + custom parameters. Note: The optimization carried out with OPLS4 including both defa…
View article: Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field Open
OpenFF Industry Public Dataset optimized at the (1) B3LYP-D3BJ / DZVP; (2) OpenFF-2.0.0; (3) Gaff-2.11-AM1BCC; (3) OPLS4 + default parameters; (4) OPLS4 + custom parameters. For (1) the corresponding tar.gz archive contains (a) sdf files o…
View article: Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field Open
OpenFF Industry Public Dataset optimized at the (1) B3LYP-D3BJ / DZVP; (2) OpenFF-2.0.0; (3) Gaff-2.11-AM1BCC; (3) OPLS4 + default parameters; (4) OPLS4 + custom parameters. For (1) the corresponding tar.gz archive contains (a) sdf files o…
View article: Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field
Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field Open
We introduce the Open Force Field (OpenFF)~2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which gen…
View article: Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale Open
The development of accurate transferable force fields is key to realizing the full potential of atomistic modeling in the study of biological processes such as protein-ligand binding for drug discovery. State-of-the-art transferable force …
View article: Collaborative assessment of molecular geometries and energies from the Open Force Field
Collaborative assessment of molecular geometries and energies from the Open Force Field Open
Force fields form the basis for classical molecular simulations and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small molecule chemistry makes it a…
View article: SPICE 1.1.3
SPICE 1.1.3 Open
SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. It is…
View article: SPICE 1.1.4
SPICE 1.1.4 Open
SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. It is…
View article: SPICE 1.1.2
SPICE 1.1.2 Open
SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. It is…
View article: SPICE 1.1.1
SPICE 1.1.1 Open
SPICE (Small-Molecule/Protein Interaction Chemical Energies) is a collection of quantum mechanical data for training potential functions. The emphasis is particularly on simulating drug-like small molecules interacting with proteins. It is…
View article: SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials Open
Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for trai…