Related papers: QuantumBind-RBFE: Accurate Relative Binding Free E…
The propensity score is widely used for causal inference in observational studies, but common parametric estimators can produce biased and inefficient effect estimates when model assumptions are violated. Nonparametric approaches reduce…
Bolted joints are critical in engineering for maintaining structural integrity and reliability. Accurate prediction of parameters influencing their function and behavior is essential for optimal performance. Traditional methods often fail…
Elasticities in depth, width, kernel size and resolution have been explored in compressing deep neural networks (DNNs). Recognizing that the kernels in a convolutional neural network (CNN) are 4-way tensors, we further exploit a new…
DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in [Fan et al., Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…
The majority of machine learning scoring functions used in drug discovery for predicting protein-ligand binding poses and affinities have been trained on the PDBBind dataset. However, it is unclear whether these new scoring functions are…
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the ligand apo ensemble and a rigid…
The accurate calculation and uncertainty quantification of the characteristics of spent nuclear fuel (SNF) play a crucial role in ensuring the safety, efficiency, and sustainability of nuclear energy production, waste management, and…
This study investigates the application of deep learning models-recurrent neural networks, gated recurrent units, and long short-term memory networks-for predicting nuclear binding energies. Utilizing data from the Atomic Mass Evaluation…
Protein folding neural networks (PFNNs) such as AlphaFold predict remarkably accurate structures of proteins compared to other approaches. However, the robustness of such networks has heretofore not been explored. This is particularly…
\citet{farrell2021deep} establish non-asymptotic high-probability bounds for general deep feedforward neural network (with rectified linear unit activation function) estimators, with \citet[Theorem 1]{farrell2021deep} achieving a suboptimal…
Material characterization in nano-mechanical tests requires precise interatomic potentials for the computation of atomic energies and forces with near-quantum accuracy. For such purposes, we develop a robust neural-network interatomic…
Probabilistic power flow (PPF) analysis is critical to power system operation and planning. PPF aims at obtaining probabilistic descriptions of the state of the system with stochastic power injections (e.g., renewable power generation and…
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free energy difference between two states. To achieve this, TFEP…
We introduce FENNIX (Force-Field-Enhanced Neural Network InteraXions), a hybrid approach between machine-learning and force-fields. We leverage state-of-the-art equivariant neural networks to predict local energy contributions and multiple…