Development of an Information System of Structures and Force Field Parameters of Chemical Compounds from Sri Lankan Flora.

Comb Chem High Throughput Screen

Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka.

Published: August 2019

Background: Sri Lanka offers a huge diversity of flora with a large proportion of those being endemic to the island. Both the endemic and native plants species serve as a rich bank of phytochemicals.

Method: In this study, "Sri Lankan Flora" an online web-based information system of phytochemical compounds isolated from the flora of Sri Lanka was proposed.

Results: The database contained 3D structures of those compounds, calculated quantitativestructure- activity relationship (QSAR) data and the GROMOS 54a7 force field parameters for each and every compound. The manually curated chemical structures, activities and force field parameters provide a possible direct avenue for computer-aided drug discovery. The present study is a continuing project with a wider goal of building up a database, not only for assisting the computeraided drug designing process, but also for other chemical applications, as the database includes structural, physical, chemical and dynamic properties of chemical compounds of the flora of Sri Lanka. The database is freely accessible at http://science.cmb.ac.lk/tools/slflora.

Download full-text PDF

Source
http://dx.doi.org/10.2174/1386207321666181010113533DOI Listing

Publication Analysis

Top Keywords

force field
12
field parameters
12
sri lanka
12
chemical compounds
8
flora sri
8
chemical
5
development system
4
system structures
4
structures force
4
parameters chemical
4

Similar Publications

Investigation the CMP process of 6 H-SiC in HO solution with ReaxFF molecular dynamics simulation.

Sci Rep

January 2025

College of Mechanical Engineering, Zhejiang University of Technology, No.18, Chaowang Road, Hangzhou, 310014, Zhejiang Province, China.

To observe the chemical mechanical polishing (CMP) process at the atomic scale, reactive force field molecular dynamics (ReaxFF-MD) was employed to simulate the polishing of 6 H-SiC under three conditions: dry, pure water, and HO solution. This study examined the reactants on the surface of 6 H-SiC during the reaction in the HO solution, along with the dissociation and adsorption processes of HO and water molecules. The mechanisms for atom removal during the CMP process were elucidated.

View Article and Find Full Text PDF

Adaptive deep brain stimulation (DBS) provides individualized therapy for people with Parkinson's disease (PWP) by adjusting the stimulation in real-time using neural signals that reflect their motor state. Current algorithms, however, utilize condensed and manually selected neural features which may result in a less robust and biased therapy. In this study, we propose Neural-to-Gait Neural network (N2GNet), a novel deep learning-based regression model capable of tracking real-time gait performance from subthalamic nucleus local field potentials (STN LFPs).

View Article and Find Full Text PDF

End-Point Affinity Estimation of Galectin Ligands by Classical and Semiempirical Quantum Mechanical Potentials.

J Chem Inf Model

January 2025

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences & IOCB Research Centre, Flemingovo nám. 2, 166 10 Prague, Czech Republic.

The use of quantum mechanical potentials in protein-ligand affinity prediction is becoming increasingly feasible with growing computational power. To move forward, validation of such potentials on real-world challenges is necessary. To this end, we have collated an extensive set of over a thousand galectin inhibitors with known affinities and docked them into galectin-3.

View Article and Find Full Text PDF

Gradient porous carbon has become a potential electrode material for energy storage devices, including the aqueous zinc-ion hybrid capacitor (ZIHC). Compared with the sufficient studies on the fabrication of ZIHCs with high electrochemical performance, there is still lack of in-depth understanding of the underlying mechanisms of gradient porous structure for energy storage, especially the synergistic effect of ultramicropores (<1 nm) and micropores (1-2 nm). Here, we report a design principle for the gradient porous carbon structure used for ZIHC based on the data-mining machine learning (ML) method.

View Article and Find Full Text PDF

Nanofriction plays an important role in the performance and lifetime of n-type or p-type TMD-based semiconductor nanodevices. However, the mechanism of nanofriction in n-type and p-type TMD semiconductors under an electric field is still blurry. In this paper, monolayers of n-MoSe and p-WSe materials were prepared by chemical vapor deposition (CVD), and their nanofriction behavior under positive electric field was investigated.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!