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Machine learning models have found numerous successful applications in computational drug discovery. A large body of these models represents molecules as sequences since molecular sequences are easily available, simple, and informative. The…

Proteins are macromolecules which hardly act alone; they need to make interactions with some other proteins to do so. Numerous factors are there which can regulate the interactions between proteins [4]. Here in this present study we aim to…

Collagen fibrils are the building block of many biological tissues, which viability depend on the fibrils properties. Altered properties of collagen fibrils are central to the appearance of many diseases, while physiological or native…

We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…

The Fenna Mathews Olson (FMO) complex of green sulphur bacteria is an example of a photosynthetic pigment protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient…

Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…

In a recent work we have briefly introduced a new structural index for water that, unlike previous indicators, was devised specifically for generic contexts beyond bulk conditions, making it suitable for hydration and nanoconfinement…

Boron phosphide (BP) is a (super)hard semiconductor constituted of light elements, which is promising for high demand applications at extreme conditions. The behavior of BP at high temperatures and pressures is of special interest but is…

Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…

It was reported that buffalo is a low susceptibility species resisting to prion diseases, which are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species. In molecular structures, TSE…

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…

Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…

Small molecules that interact strongly with water were the subject of this molecular dynamics (MD) study. These solutes include a cryoprotectant (DMSO), a polyalcohol [CH$_2$(OH)$_2$], carboxylic acid conjugates (HCOOH and HCOONa), an…

The rise of cost involved with drug discovery and current speed of which they are discover, underscore the need for more efficient structure-based drug design (SBDD) methods. We employ Generative Flow Networks (GFlowNets), to effectively…

Functional nano-templates enable self-assembly of otherwise impossible arrangements of molecules. A particular class of such templates is that of sp2 hybridized single layers of hexagonal boron nitride or carbon (graphene) on metal…

Protein-ligand binding complexes are ubiquitous and essential to life. Protein-ligand binding affinity prediction (PLA) quantifies the binding strength between ligands and proteins, providing crucial insights for discovering and designing…

Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein…

Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…

A sequential of concepts developed in last decade has enabled a resolution to multiple anomalies of water ice and its low-dimensionality, particularly. Developed concepts include the coupled hydrogen bond oscillator pair, segmental specific…

By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these…