Journal of chemical information and modeling
Nov 23, 2020
Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydro...
Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between ato...
We have employed our bioinformatics workbench, named Evolution, a Multi-Agent System based architecture with lattice-bead-models, evolutionary-algorithms, and correlated-networks as inhomogeneous spaces, with different correlation lengths, mimicking ...
Despite the importance of amyloid formation in disease pathology, the understanding of the primary structure?activity relationship for amyloid-forming peptides remains elusive. Here we use a new neural-network based method of analysis: the classifyin...
Saponins are a type of compounds bearing a hydrophobic steroid/triterpenoid moiety and hydrophilic carbohydrate branches. The majority of the saponins demonstrate a broad range of prominent pharmacological activities. Nevertheless, many saponins also...
Journal of molecular graphics & modelling
Jun 1, 2019
BACKGROUND: The activation of follicle stimulating hormone receptor (FSHR) by FSH and the consequent downstream signaling activities are crucial for reproductive health. The role of FSHR in tumor progression as well as osteoporosis advancement has al...
Journal of chemical information and modeling
Mar 25, 2019
In this work, we propose a machine learning approach to generate novel molecules starting from a seed compound, its three-dimensional (3D) shape, and its pharmacophoric features. The pipeline draws inspiration from generative models used in image ana...
The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to det...
International journal of pharmaceutics
Dec 20, 2018
Nanostructured lipid carriers (NLC) are biocompatible and biodegradable nanoscale systems with extensive application for controlled drug release. However, the development of optimal nanosystems along with a reproducible manufacturing process is still...
Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep lear...