生物大分子
Kinase-targeted drug design is challenging. It requires designing inhibitors that can bind to specific kinases when all kinase catalytic domains share a common folding scaffold that binds ATP. Thus, obtaining the desired selectivity, given…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Graph neural networks (GNNs) have been proposed for a wide range of graph-related learning tasks. In particular, in recent years, an increasing number of GNN systems were applied to predict molecular properties. However, a direct impediment…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial…
In recent years, fossil-based fuels have been used to supply the energy needs of the world. Fossil-based fuels induce accumulation of the atmospheric CO2 which causes global warming. One of CO2 source is flue gas emission from the power…
The endogenous tridecapeptide neurotensin (NT) has emerged as an important inhibitory modulator of pain transmission, exerting its analgesic action through the activation of the G protein-coupled receptors, NTS1 and NTS2. Whereas both NT…
Polyampholyte field theory and explicit-chain molecular dynamics models of sequence-specific phase separation of a system with two intrinsically disordered protein (IDP) species indicate consistently that a substantial polymer excluded…
Protein aggregates in the brain play a central role in cognitive decline and structural damage associated with neurodegenerative diseases. For instance, in Alzheimer's disease the formation of Amyloid-beta plaques and tau proteins…
The anticancer potential of monoamine oxidase (MAO) was observed in pre-clinical assays conducted with cell cultures and animals. L-Deprenyl (DEP) causes apoptosis in melanoma, leukemia and mammary cells. High-dose DEP has shown toxicity in…
Hyperactivity is one of the hallmakrs of ADHD. Aberrant dopamine signaling is a major theme in ADHD and dopamine production is directly linked to the intensity and persistence of hyperactive conduct. The strength and persistence of…
In this study, the mechanical behavior of single tau, dimerized tau, and tau-microtubule interface subjected to high strain rate is investigated by molecular dynamics simulation.
Molecular structures of RNA molecules reconstructed from X-ray crystallography frequently contain errors. Motivated by this problem we examine clustering on a torus since RNA shapes can be described by dihedral angles. A previously…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
There is an urgent need of biosynthetic bone grafts with enhanced osteogenic capacity. In this study, we describe the design of hierarchical meso-macroporous 3D-scaffolds based on mesoporous bioactive glasses (MBGs), enriched with the…
Protein-protein interactions are the basis of many important physiological processes and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitor of apoptosis proteins (IAPs)-mediated interactions are…
Searching for novel molecules with desired chemical properties is crucial in drug discovery. Existing work focuses on developing neural models to generate either molecular sequences or chemical graphs. However, it remains a big challenge to…
In the drug repurposing approach, the chemically diverse and potentially safe molecules can be explored as therapeutic potential out of those originally targeted indications. However, the intellectual property rights, and competitive…
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…