AI Article Synopsis
Article Abstract
This paper presents a formal data publishing platform for computational chemistry using semantic web technologies. This platform encapsulates computational chemistry data from a variety of packages in an Extensible Markup Language (XML) file called CSX (Common Standard for eXchange). On the basis of a Gainesville Core (GC) ontology for computational chemistry, a CSX XML file is converted into the JavaScript Object Notation for Linked Data (JSON-LD) format using an XML Stylesheet Language Transformation (XSLT) file. Ultimately the JSON-LD file is converted to subject-predicate-object triples in a Turtle (TTL) file and published on the web portal. By leveraging semantic web technologies, we are able to place computational chemistry data onto web portals as a component of a Giant Global Graph (GGG) such that computer agents, as well as individual chemists, can access the data.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.jpca.6b10489 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation.
Biophys J
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States. Electronic address:
Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems.
View Article and Find Full Text PDFUnderstanding pectin cross-linking in plant cell walls.
Commun Biol
January 2025
Department of Chemistry, University of Warwick, Coventry, UK.
Pectin is a major component of plant cells walls. The extent to which pectin chains crosslink with one another determines crucial properties including cell wall strength, porosity, and the ability of small, biologically significant molecules to access the cell. Despite its importance, significant gaps remain in our comprehension, at the molecular level, of how pectin cross-links influence the mechanical and physical properties of cell walls.
View Article and Find Full Text PDFLipidic folding pathway of α-Synuclein via a toxic oligomer.
Nat Commun
January 2025
NMR Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
Aggregation intermediates play a pivotal role in the assembly of amyloid fibrils, which are central to the pathogenesis of neurodegenerative diseases. The structures of filamentous intermediates and mature fibrils are now efficiently determined by single-particle cryo-electron microscopy. By contrast, smaller pre-fibrillar α-Synuclein (αS) oligomers, crucial for initiating amyloidogenesis, remain largely uncharacterized.
View Article and Find Full Text PDFUnderstanding the Mechanism of Electrochemical CO Capture by Supercapacitive Swing Adsorption.
ACS Nano
January 2025
Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
Carbon dioxide capture underpins an important range of technologies that can help to mitigate climate change. Improved carbon capture technologies that are driven by electrochemistry are under active development, and it was recently found that supercapacitor energy storage devices can reversibly capture and release carbon dioxide. So-called supercapacitive swing adsorption (SSA) has several advantages over traditional carbon dioxide capture technologies such as lower energy consumption and the use of nontoxic materials.
View Article and Find Full Text PDFApproximate Hamiltonians from a Linear Vibronic Coupling Model for Solution-Phase Spin Dynamics.
J Chem Theory Comput
January 2025
Department of Chemistry, The University of Manchester, Manchester M13 9PL, U.K.
The linear vibronic coupling (LVC) model is an approach for approximating how a molecular Hamiltonian changes in response to small changes in molecular geometry. The LVC framework thus has the ability to approximate molecular Hamiltonians at low computational expense but with quality approaching multiconfigurational calculations, when the change in geometry compared to the reference calculation used to parametrize it is small. Here, we show how the LVC approach can be used to project approximate spin Hamiltonians of a solvated lanthanide complex along a room-temperature molecular dynamics trajectory.
View Article and Find Full Text PDFWant 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!