HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the effective representation of molecular structures and interactions in protein-ligand binding. We design an end-to-end pipeline for high-throughput screening and lead optimization, targeting applications in structure-based drug design. We assess our approach using established public benchmarks based on the CASF 2016 core set, achieving top-tier results in affinity and pose prediction (Pearson's r = 0.86, RMSE = 1.15, Top-1 = 0.95). Furthermore, we utilize a novel interaction profiling approach to identify potential biases in the model and dataset to boost interpretability and support the unbiased nature of our method. Finally, we showcase HydraScreen's capacity to generalize across unseen proteins and ligands, offering directions for future development of robust machine learning scoring functions. HydraScreen (accessible at https://hydrascreen.ro5.ai) provides a user-friendly GUI and a public API, facilitating easy assessment of individual protein-ligand complexes

Relativistic dynamics of a quantum system

ISSN Online: 2327-4379In this paper, we examine quantum systems with relativistic dynamics. We show that for a successful description of these systems, the application of Ga-lilei invariant nonrelativistic Hamiltonian is necessary. To modify this Ha-miltonian to relativistic dynamics, we require precise relativistic kinetic ener-gy operators instead of nonrelativistic ones for every internal (Jacobi) coordi-nate. Finally, we introduce and investigate the Schrödinger equation with re-lativistic dynamics for two-particle systems with harmonic oscillator and Coulomb potentialsFizikos katedraVytauto Didžiojo universiteta

Verification of boundaries for the application theory to a simple two-particle case having exact solution

ISSN 0024-2969 - neteisingas; nuo 2003 m. - ISSN 1648-850

Kinematic relativity of quantum mechanics: free particle with different boundary conditions

ISSN Online: 2327-4379An investigation of origins of the quantum mechanical momentum operator has shown that it corresponds to the nonrelativistic momentum of classical special relativity theory rather than the relativistic one, as has been unconditionally believed in traditional relativistic quantum mechanics until now. Taking this correspondence into account, relativistic momentum and energy operators are defined. Schrödinger equations with relativistic kinematics are introduced and investigated for a free particle and a particle trapped in the deep potential wellFizikos katedraVytauto Didžiojo universiteta

Генеалогические коэффициенты микроскопических моделей атомного ядра

ISSN 0024-2969 - neteisingas; nuo 2003 m. - ISSN 1648-8504Vytauto Didžiojo universiteta

Ground state nucleon, dark energy and dark matter

ISSN Online: 2327-4379The recently introduced model of the nucleon as a system of three point particles predicts all characteristics of the proton and neutron with experimental precision only at condition that nucleon is the loosely bound state in system of deep potential wells. The model’s Hamiltonian contains ground state with the same parity and spin as the nucleon but with other different characteristics. Existence of this ground state nucleon means that the visible Universe is composed of excited matter. The direct transition between excited and ground states is strictly forbidden, however, stimulated emission can ignite such process. Most likely, corresponding conditions realize at supernova explosion. It is shown that presence of this matter, composed of ground state nucleons, in Universe gives the chance for consistent explanation of dark matter and dark energy phenomenaFizikos katedraVytauto Didžiojo universiteta

On the types of collective motions in an electronic atom shell

ISSN 0024-2969 - neteisingas; nuo 2003 m. - ISSN 1648-8504Fizikos instituta

Reduced-Hamiltonian method in the theory of bound states of systems of identical particles

ISSN 0090-4759; ISSN of Original: 0367-2026. Žurn. pavadinimas pasikeitė į Physics of Particles and Nuclei Letters, ISSN 1547-4771 (Print), 1531-8567 (Online)The Schrodinger equation for a system of identical particles has a hidden symmetry due to the indistinguishability of the particles. This symmetry can be used to eliminate the antisymmetrization operator from the equation and to obtain functional differential equations for the components of the wave function. In these equations there remains only a reduced two-particle Hamiltonian which is the minimal essential part of the many-particle Hamiltonian. The review is devoted to an exposition of the consequences of the symmetry and to a method of solution of functional differential equations for bound states of a system based on expansion of the components with respect to a complete basis of eigenfunctions of the reduced HamiltonianFizikos instituta