Amyotrophic lateral sclerosis (ALS) is a devastating and progressive neurodegenerative disease with limited treatment options available. Cerebrolysin is a drug candidate for the treatment of ALS because of its neuroprotective and neuroregenerative ef...
Several experimental evidences have shown that the human endogenous hormones can interact with drugs in many ways and affect drug efficacy. The hormone drug interactions (HDI) are essential for drug treatment and precision medicine; therefore, it is ...
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at in...
BACKGROUND: Predicting protein-protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings from protein language models, wh...
Journal of chemical information and modeling
38623916
Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical m...
Protein science : a publication of the Protein Society
38532692
We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activit...
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases w...
Journal of chemical information and modeling
38739853
Currently, antimicrobial resistance constitutes a serious threat to human health. Drugs based on antimicrobial peptides (AMPs) constitute one of the alternatives to address it. Shallow and deep learning (DL)-based models have mainly been built from a...
International journal of molecular sciences
38892439
Enzymes play a crucial role in various industrial production and pharmaceutical developments, serving as catalysts for numerous biochemical reactions. Determining the optimal catalytic temperature () of enzymes is crucial for optimizing reaction cond...
Journal of chemical information and modeling
38829726
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can n...