Biomolecules
Opioid use disorder (OUD) is a chronic and relapsing condition that involves the continued and compulsive use of opioids despite harmful consequences. The development of medications with improved efficacy and safety profiles for OUD…
Atlantic sea lamprey contains two corticoid receptors (CRs), CR1 and CR2, that are identical except for a four amino acid insert (Thr-Arg-Gln-Gly) in the CR1 DNA-binding domain (DBD). Steroids are stronger transcriptional activators of CR2…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
Lycopene contributes to the red-colored pigmentation of fruits and vegetables, and it is a fat-soluble carotenoid with antioxidant properties. Epidemiological studies have shown the significant health benefits associated to the consumption…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Molecular docking, given a ligand molecule and a ligand binding site (called ``pocket'') on a protein, predicting the binding mode of the protein-ligand complex, is a widely used technique in drug design. Many deep learning models have been…
The information content of symbolic sequences (such as nucleic- or amino acid sequences, but also neuronal firings or strings of letters) can be calculated from an ensemble of such sequences, but because information cannot be assigned to…
This paper focuses on three critical problems on protein classification. Firstly, Carbohydrate-active enzyme (CAZyme) classification can help people to understand the properties of enzymes. However, one CAZyme may belong to several classes.…
Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…
The linear sequence of amino acids determines protein structure and function. Protein design, known as the inverse of protein structure prediction, aims to obtain a novel protein sequence that will fold into the defined structure. Recent…
Activity cliffs (ACs), which are generally defined as pairs of structurally similar molecules that are active against the same bio-target but significantly different in the binding potency, are of great importance to drug discovery. Up to…
Structure-based drug design, i.e., finding molecules with high affinities to the target protein pocket, is one of the most critical tasks in drug discovery. Traditional solutions, like virtual screening, require exhaustively searching on a…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with…
The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor. The receptor is activated by a small peptide ligand neurotensin. NTSR1 can be expressed in HEK cells by stable transfection. Previously we used the fluorescent…
Glutamate-gated kainate receptors (KARs) are ubiquitous in the central nervous system of vertebrates, mediate synaptic transmission on post-synapse, and modulate transmitter release on pre-synapse. In the brain, the trafficking, gating…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Nanoencapsulation has become a widespread technique to improve the bioavailability of bioactive compounds like lycopene. Consumption of lycopene rich foods is effective in preventing cancer, diabetes, and cardiovascular diseases due to its…
The use of biodegradable polymers simplifies the development of therapeutic devices with regards to transient implants and three-dimensional platform suitable for tissue engineering. Further advances have also occurred in the controlled…