We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/ci100052b | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Enantioselective OTUD7B fragment discovery through chemoproteomics screening and high-throughput optimisation.
Commun Chem
January 2025
Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.
Deubiquitinating enzymes (DUBs) are key regulators of cellular homoeostasis, and their dysregulation is associated with several human diseases. The ovarian tumour protease (OTU) family of DUBs are biochemically well-characterised and of therapeutic interest, yet only a few tool compounds exist to study their cellular function and therapeutic potential. Here we present a chemoproteomics fragment screening platform for identifying novel DUB-specific hit matter, that combines activity-based protein profiling with high-throughput chemistry direct-to-biology optimisation to enable rapid elaboration of initial fragment hits against OTU DUBs.
View Article and Find Full Text PDFA twofold perspective on the quality of research publications: The use of ICTs and research activity models.
PLoS One
January 2025
Department of Structural and Molecular Biology, University College London, London, United Kingdom.
Previous studies have highlighted the inherent subjectivity, complexity, and challenges associated with research quality leading to fragmented findings. We identified determinants of research publication quality in terms of research activities and the use of information and communication technologies by employing an interdisciplinary approach. We conducted web-based surveys among academic scientists and applied machine learning techniques to model behaviors during and after the COVID-19 pandemic.
View Article and Find Full Text PDFSurface decorated metal carbonyl clusters: bridging organometallic molecular clusters and atomically precise ligated nanoclusters.
Dalton Trans
January 2025
Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Via P. Gobetti 85, 40129 Bologna, Italy.
In this Frontier Article, the work carried out within our research group in Bologna in the field of surface decorated metal carbonyl clusters will be outlined and put in a more general context. After a short Introduction, clusters composed of a metal carbonyl core decorated on the surface by metal-ligand fragments will be analyzed. Both metal-ligand fragments behaving as Lewis acids and Lewis bases will be considered.
View Article and Find Full Text PDFFragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology.
J Cheminform
January 2025
Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK.
Current strategies centred on either merging or linking initial hits from fragment-based drug design (FBDD) crystallographic screens generally do not fully leaverage 3D structural information. We show that an algorithmic approach (Fragmenstein) that 'stitches' the ligand atoms from this structural information together can provide more accurate and reliable predictions for protein-ligand complex conformation than general methods such as pharmacophore-constrained docking. This approach works under the assumption of conserved binding: when a larger molecule is designed containing the initial fragment hit, the common substructure between the two will adopt the same binding mode.
View Article and Find Full Text PDFEchocardiographic phenotypes of diabetic myocardial disorder: evolution over 15 months follow-up in the ARISE-HF trial.
Cardiovasc Diabetol
January 2025
Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Background: Diabetic myocardial disorder (DbMD, evidenced by abnormal echocardiography or cardiac biomarkers) is a form of stage B heart failure (SBHF) at high risk for progression to overt HF. SBHF is defined by abnormal LV morphology and function and/or abnormal cardiac biomarker concentrations.
Objective: To compare the evolution of four DbMD groups based on biomarkers alone, systolic and diastolic dysfunction alone, or their combination.
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!