GenerationE of huge "omics" data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatu...
Development of new antimicrobial agents is a good solution to overcome drug-resistance problems. From this perspective, new quinoxaline derivatives bearing various bioactive heterocyclic moieties (thiadiazoles, oxadiazoles, pyrazoles and thiazoles) w...
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Journal of chemical information and modeling
29425456
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geomet...
Journal of biomolecular structure & dynamics
29471734
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associ...
We present two approaches for the computation of hydrogen bond acceptor strengths, one by machine-learning and one by a composite quantum-mechanical protocol, both based on the well-established pK scale and dataset. The QM calculations after a necess...
Proceedings of the National Academy of Sciences of the United States of America
30808805
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing G...
Journal of chemical information and modeling
30762364
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...
Inspecting protein and ligand electrostatic potential (ESP) surfaces in order to optimize electrostatic complementarity is a key activity in drug design. These ESP surfaces need to reflect the true electrostatic nature of the molecules, which typical...
Protein science : a publication of the Protein Society
31642127
Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding side-chain functional groups which maximize transition-state stabilization, and then sear...