scholarly journals SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W652-W656 ◽  
Author(s):  
M. Hattori ◽  
N. Tanaka ◽  
M. Kanehisa ◽  
S. Goto
Keyword(s):  
Chemical Structure ◽  
Network Analyses ◽  
Structure Search

scholarly journals Identification of new superwarfarin-type rodenticides by structural similarity. The docking of ligands on the vitamin K epoxide reductase enzyme’s active site

2015 ◽  
Vol 7 (1) ◽  
pp. 108-122
Author(s):  
László Ferencz ◽  
Daniela Lucia Muntean
Keyword(s):  
Vitamin K ◽  
Chemical Structure ◽  
Enzyme Inhibitors ◽  
Structural Similarity ◽  
Vitamin K Epoxide Reductase ◽  
Pubchem Compound ◽  
Structure Search ◽  
Epoxide Reductase ◽  
Compound Database ◽  
Similarity Thresholds

Abstract The rodenticide brodifacoum is highly toxic to mammals and birds, and extremely toxic to fish. It is a highly cumulative poison due to its high lipophilicity and extremely slow elimination. For this reason, it may be interesting to find similar compounds in order to enlarge the spectrum of vitamin K epoxide reductase enzyme inhibitors used today in pest control. We used the Similar Compounds search type of the Chemical Structure Search of the PubChem Compound Database to locate records that are similar to the chemical structure of brodifacoum, using pre-specified similarity thresholds. Using the threshold ≥ than 95% for the similar structures criteria, we found 14 compounds (from over 30 million entries) that meet this criteria. Two of these compounds have a better binding affinity to vitamin K epoxide reductase enzyme than brodifacoum, but the binding energy of the other 12 substances is also high, having identical or lower lipophilicity; consequently, they will eliminate faster, possibly lacking a part of the adverse effects.

scholarly journals Correction to: Interoperable chemical structure search service

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Miroslav Kratochvíl ◽  
Jiří Vondrášek ◽  
Jakub Galgonek
Keyword(s):  
Chemical Structure ◽  
Structure Search ◽  
Search Service

scholarly journals Interoperable chemical structure search service

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Miroslav Kratochvíl ◽  
Jiří Vondrášek ◽  
Jakub Galgonek
Keyword(s):  
Chemical Structure ◽  
Query Language ◽  
Search Space ◽  
Chemical Databases ◽  
Search Terms ◽  
Structure Search ◽  
Search Service ◽  
Large Databases ◽  
Similarity Searches ◽  
Small Molecule Databases

Abstract Motivation The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases provides a way to efficiently utilize these resources. To simplify such searches, many databases have adopted semantic technologies that allow interoperable querying of the datasets using SPARQL query language. However, the interoperable interfaces of the chemical databases still lack the functionality of structure-driven chemical search, which is a fundamental method of data discovery in the chemical search space. Results We present a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible. The service thus offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms. Availability The service is freely available and accessible using a standard SPARQL endpoint interface. The service documentation and user-oriented demonstration interfaces that allow quick explorative querying of datasets are available at https://idsm.elixir-czech.cz.

CHEMLINE: a Chemical Structure Search Key to Biological Information

1978 ◽  
pp. 58-72
Author(s):  
MELVIN L. SPANN ◽  
DONALD J. HUMMEL ◽  
ROBERT J. SCHULTHEISZ ◽  
SHARON L. VALLEY ◽  
DONALD F. WALKER
Keyword(s):  
Chemical Structure ◽  
Biological Information ◽  
Structure Search

Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program

Chirality ◽  
2016 ◽  
Vol 28 (5) ◽  
pp. 370-375 ◽  
Author(s):  
Hiroshi Izumi ◽  
Laurence A. Nafie ◽  
Rina K. Dukor
Keyword(s):  
Chemical Structure ◽  
Organic Molecules ◽  
Three Dimensional ◽  
Structure Search

Inelastic Electron-Matter Interactions

1978 ◽  
Vol 36 (3) ◽  
pp. 259-267
Author(s):  
J. Silcox
Keyword(s):  
Electron Microscope ◽  
Energy Loss ◽  
Chemical Structure ◽  
Inelastic Electron ◽  
Primary Concern ◽  
Unique Probe ◽  
Introductory Paper ◽  
Elastic Processes ◽  
Experimental Level ◽  
Inelastic Processes

In this introductory paper, my primary concern will be in identifying and outlining the various types of inelastic processes resulting from the interaction of electrons with matter. Elastic processes are understood reasonably well at the present experimental level and can be regarded as giving information on spatial arrangements. We need not consider them here. Inelastic processes do contain information of considerable value which reflect the electronic and chemical structure of the sample. In combination with the spatial resolution of the electron microscope, a unique probe of materials is finally emerging (Hillier 1943, Watanabe 1955, Castaing and Henri 1962, Crewe 1966, Wittry, Ferrier and Cosslett 1969, Isaacson and Johnson 1975, Egerton, Rossouw and Whelan 1976, Kokubo and Iwatsuki 1976, Colliex, Cosslett, Leapman and Trebbia 1977). We first review some scattering terminology by way of background and to identify some of the more interesting and significant features of energy loss electrons and then go on to discuss examples of studies of the type of phenomena encountered. Finally we will comment on some of the experimental factors encountered.

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