Related papers: Exploring PROTAC cooperativity with coarse-grained…
Proteolysis targeting chimeras (PROTACs) are small molecules that trigger the breakdown of traditionally ``undruggable'' proteins by binding simultaneously to their targets and degradation-associated proteins. A key challenge in their…
PROteolysis TArgeting Chimeras (PROTACs) are an emerging therapeutic modality for degrading a protein of interest (POI) by marking it for degradation by the proteasome. Recent developments in artificial intelligence (AI) suggest that deep…
Proteolysis-targeting chimeras (PROTACs) represent a promising therapeutic modality that induces targeted protein degradation by hijacking the ubiquitin-proteasome system. However, rational PROTAC design remains challenging due to the…
Proteolysis-Targeting Chimeras (PROTACs) represent a novel class of small molecules which are designed to act as a bridge between an E3 ligase and a disease-relevant protein, thereby promoting its subsequent degradation. PROTACs are…
PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise,…
Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target…
Targeted protein degradation (TPD) is a rapidly growing field in modern drug discovery that aims to regulate the intracellular levels of proteins by harnessing the cell's innate degradation pathways to selectively target and degrade…
The imperfect modeling of ternary complexes has limited the application of computer-aided drug discovery tools in PROTAC research and development. In this study, an AI-assisted approach for PROTAC molecule design pipeline named LM-PROTAC…
Understanding E3 ligase and target substrate interactions are important for cell biology and therapeutic development. However, experimental identification of E3 target relationships is not an easy task due to the labor-intensive nature of…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification…
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable". Proteolysis-targeting chimeras (PROTACs) and molecular…
PROTACs, as a highly promising new. therapeutic paradigm, have attracted widespread attention from the academic and pharmaceutical communities in recent years. To date, the design and validation of PROTACs molecule's druggability primarily…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
The computational homogenization of elastoplastic polycrystals is a challenging task due to the huge number of grains required, their complicated interactions and due to the complexity of crystal plasticity models per se. Despite a few…