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The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL)…
Particle Dobble is an open-access, gamified learning tool designed to address persistent misconceptions in particle physics education by symbolically representing elements of the Standard Model. Aimed at upper secondary and introductory…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
ColorShapeLinks is an AI board game competition framework specially designed for students and educators in videogame development, with openness and accessibility in mind. The competition is based on an arbitrarily-sized version of the…
Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Recent advances have incorporated deep learning techniques to…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…
Molecular docking aims to predict the 3D pose of a small molecule in a protein binding site. Traditional docking methods predict ligand poses by minimizing a physics-inspired scoring function. Recently, a diffusion model has been proposed…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…
Existing protein-ligand docking studies typically focus on the self-docking scenario, which is less practical in real applications. Moreover, some studies involve heavy frameworks requiring extensive training, posing challenges for…
Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
The purpose of this work is to explore a teaching methodology aimed at communicating topics and subjects not typically studied and analyzed in the (Italian) secondary school. We focused specifically on the use of videogames as a…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…
This paper presents results from the design and testing of an educational version of Quantum Moves, a Scientific Discovery Game that allows players to help solve authentic scientific challenges in the effort to develop a quantum computer.…
Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…
This article proposes and discusses qualitatively the use of a didactic board game in Science Education for high school students. The game contemplates in an interdisciplinary way the areas of Physics, Biology, Chemistry and Astronomy and…