Related papers: Application of Information Spectrum Method on Smal…
The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based…
Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to transfer information among bio-nano devices. In this paper, we focus on the detection problem for biological MC receivers employing ligand…
This article proposes a novel computational modeling approach for short-ranged molecular interactions between curved slender fibers undergoing large 3D deformations, and gives a detailed overview how it fits into the framework of existing…
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
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…
Predicting interactions between small molecules and proteins is a crucial ingredient of the drug discovery process. In particular, accurate predictive models are increasingly used to preselect potential lead compounds from large molecule…
We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate…
Understanding the extent of contact between objects is crucial for surface-driven phenomena in the natural world. While interactions are known to occur at subnanometer-length scales, the techniques needed to measure such small-length scales…
Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a…
Small molecules play a pivotal role in modern medicine, and scrutinizing their interactions with protein targets is essential for the discovery and development of novel, life-saving therapeutics. The term "bioactivity" encompasses various…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
Molecular representation learning is pivotal for various molecular property prediction tasks related to drug discovery. Robust and accurate benchmarks are essential for refining and validating current methods. Existing molecular property…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
In neuroscience, methods from information geometry (IG) have been successfully applied in the modelling of binary vectors from spike train data, using the orthogonal decomposition of the Kullback-Leibler divergence and mutual information to…
We have earlier reported the iMOLSDOCK technique to perform induced-fit peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLS) technique to sample the conformation and the docking pose of the small molecule…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
Understanding how features interact with each other is of paramount importance in many scientific discoveries and contemporary applications. Yet interaction identification becomes challenging even for a moderate number of covariates. In…
Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…
This contribution proposes the first 3D beam-to-beam interaction model for molecular interactions between curved slender fibers undergoing large deformations. While the general model is not restricted to a specific beam formulation, in the…
Summary: Founded upon diffusion with damping, ITM Probe is an application for modeling information flow in protein interaction networks without prior restriction to the sub-network of interest. Given a context consisting of desired origins…