Activity landscape (AL) models are used for visualizing and interpreting structure-activity relationships (SARs) in compound datasets. Therefore, ALs are designed to present chemical similarity and compound potency information in context. Different t...
Driven by rapid advances in computer hardware and publicly available datasets over the past decade, deep learning has achieved tremendous success in the transformation of many computational disciplines. These novel technologies have had considerable ...
Artificial intelligence (AI) and machine learning, in particular, have gained significant interest in many fields, including pharmaceutical sciences. The enormous growth of data from several sources, the recent advances in various analytical tools, a...
Journal of chemical information and modeling
Jul 24, 2020
Deep learning approaches have become popular in recent years in the field of molecular design. While a variety of different methods are available, it is still a challenge to assess and compare their performance. A particularly promising approach for...
INTRODUCTION: After the initial wave of antibiotic discovery, few novel classes of antibiotics have emerged, with the latest dating back to the 1980's. Furthermore, the pace of antibiotic drug discovery is unable to keep up with the increasing preval...
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
Jun 16, 2020
Several proteins including S-nitrosoglutathione reductase (GSNOR), complement Factor D, complement 3b (C3b) and Protein Kinase R-like Endoplasmic Reticulum Kinase (PERK), have been demonstrated to be involved in pathogenesis pathways for Alzheimer's ...
Journal of chemical theory and computation
Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Interdisciplinary sciences, computational life sciences
Jun 1, 2020
A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence abou...
The industrial revolution that began in the late 1800s has resulted in dramatic changes in the environment, human lifestyle, dietary habits, social structure, and so on. Almost certainly because this rapid evolution has outpaced the ability of the bo...
Journal of chemical information and modeling
May 11, 2020
We present a new approach to estimate the binding affinity from given three-dimensional poses of protein-ligand complexes. In this scheme, every protein-ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributi...