Options Identical Structures Similar Compounds, score >= 95% Similar Compounds, score >= 90% Similar Compounds, score >= 80% Identical Structures Similar Structures with  same connectivity any tautomer same stereoisomer same isotopical labels same stereochemistry and isotopes non-conflicting stereochemistry same isotopes and non-conflicting stereoisomers   threshold >=  99% 98% 97% 96% 95% 93% 90% 85% 80% 70% 60%   Substructure Superstructure Substructure Superstructure match stereochemistry  Ignore Exact Relative Nonconflicting  and  Match isotopes Match charges Match tautomers Ringsystems not embedded Single/double bonds match aromatic bonds Chain bonds match ring bonds Strip hydrogen   Molecular Formula with  exact stoichiometry allow other element   Sort results by: Shape-then-featureFeature-then-shapeShape-and-featureConformer Id Output to: PubChem 3D Alignment ViewerNCBI EntrezTable Summary Time Limit(seconds):  unlimited 30 60 90 300 600 3,600      Result Limit: 10 50 100 500 1,000 10,000 100,000 2,000,000  

PubChem Substructure FingerprintV1.3 http://pubchem.ncbi.nlm.nih.govPage 4 of 21 5/1/2009 7:21:06 AM PubChem Substructure Fingerprint Description (cont.)

Tanimoto coefficient6-8

Search resultsItems: 1 to 20 of 1545467

OPEN CHEMISTRY DATABASE SEARCH 1.0 βETA Current System 

Partition coefficient log P in −0.4 to +5.6 range

MeSH (Medical Subject Headings)

DrugBank CAMEO Chemicals The National Institute for Occupational Safety and Health - NIOSH HSDB ILO-ICSC Human Metabolome Database OSHA Chemical Sampling Information OSHA Occupational Chemical DB NIOSH-PocketGuide

The E-utilities are therefore the structured interface to the Entrez system

For example, a well-annotated SWISS-PROT record for a particular protein may have fields that describe other protein or GenBank records from which it was derived.

he table of contents on a PubChem summary page lists the categories of information that are available for the particular substance or compound. A PubChem Substance summary page is based on the data submitted by an individual depositor. A PubChem Compound summary page, on the other hand, displays data organized by NCBI automated data processing, serving as a hub of information for each unique chemical structure. PubChem Compound summary pages therefore tend to list more topics in their table of contents.

PubChem is organized as three interconnected databases: Substance, Compound, and BioAssay

Therefore, 3-D neighboring may offer comple-mentary views on structural similarity between molecules withsimilar biological activities.

Forexample, ChEMBL [49] manually extracts bioactivity datafrom peer-reviewed papers published in journals in themedicinal chemistry and natural product domains.

Therefore, databases need to document the provenance of the data and devise a way to notify users of that information.  In turn, users should always pay attention to the data provenance issue when using a database.  

Peak Search

Although it grew out of the relational database model

This is for mass spectrometry and chromatography data

. Ring aromaticity is handled in SMILES at the atomic level, not at the bond level (i.e. an atom is considered aromatic rather than a

All InChIs currently are prefixed with “INCHI=”. Following this, a designator of “1/” or “1S/” indicates whether the InChI is non-standard or standard (i.e. with fixed standardized options in the software)

another language, based on conventions in SMILeS, has also been devel-oped for rapid substructure searching, called SMiles arbitrary target Spec-ification (SMartS). Similarly, SMIrKS has also been defined as a subset of SMILeS that encodes reaction transforms. SMIrKS does not have a defini-tion, but plays on the SMILeS acronym. SMartS and SMIrKS will be consid-ered in more detail in later chapters.

Rings are represented by breaking one single or aromatic bond in each ring, and designating this ring-closure point with a digit immediately following the atoms connected through the broken bond.Atoms in aromatic rings are specified by lower cases letters.Therefore, cyclohexane and benzene can be represented by the following SMILES

As a starting point, this section will introduce a simplified form of connection table, which we’ll call an “SCT”. This SCT does not correspond directly to any existing file format (at least as far as we know!). Rather, it is a convenient model that we will use just for the purpose of this demonstration.

Another notation, called rep-resentation of structure diagram arranged linearly(ROSDAL),52,53was written to transfer structuresquickly in a compact form over a network to enablesearching of the Beilstein database online.54ROSDALis still supported by InfoChem, and by Elsevier (Am-sterdam, The Netherlands) in Reaxys (vide infra) andthe Beilstein CrossFire structure editor.