8 papers · ranked by Valyu relevance
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…
Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann + 1 more
Protein kinases are among the most important drug targets because their dysregulation can cause cancer, inflammatory, and degenerative diseases. Developing selective inhibitors is challenging due to the highly conserved binding sites across the roughly 500 human kinases. Thus, detecting subtle similarities on a…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Andrew Simmonett, Bernard Brooks, Thomas Darden
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which…
William Godinez, Eric Ma, Alexander Chao, Luying Pei + 6 more
Recent advances in generative modeling allow designing novel compounds through deep neural networks. One such neural network model, the Junction Tree Variational Auto- Encoder (JT-VAE), excels at proposing chemically valid structures. Based on JT-VAE, we built a generative modeling approach (JAEGER) for finding novel…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Authors not listed
We present a simple yet efficient random (brute-force) algorithm for constructing solvated molecular systems. By placing solvent molecules at random positions and orientations within a simulation box, we circumvent the complexities typically associated with more sophisticated packing algorithms. The main computational…
Authors not listed
A protocol for generating potential energy surfaces and performing photoinduced nonadiabatic multidimensional wave packet propagation is presented. The workflow starts with the parameterization of a linear vibronic coupling (LVC) Hamiltonian using the BSE@GW approach. In a second step, the LVC model is used as input…