Ludovic Mayer – Database1
E2020 – Soft skills II – Information Literacy
3. Databases
01.03.2022
Mgr. Ludovic Mayer
ludovic.mayer@recetox.muni.cz
Ludovic Mayer – 3. Database2
I want to start working/writing, but …
̶ What resources to use?
̶ Where can I find them?
̶ How can I find what interest me?
̶ What to do if I don’t find what I need?
̶ How to formulate a query understood by the database?
Ludovic Mayer – 3. Database3
Content
̶ Lecture divided into 2 parts:
̶ 1st part: Theoretical – to understand how is the information stored
– how to access it
̶ 2nd part: Practical – you are at the helm and you find the information!
Ludovic Mayer – 3. Database4
VPN
̶ MUNI VPN
̶ MUNI
̶ Eduroam
https://it.muni.cz/en/services/wireless-wi-fi-connection
Ludovic Mayer – 3. Database5
Database
“a usually large collection of data organized especially for rapid search and
retrieval (as by a computer)” (Webster dictionary)
Exist for multiples types of information
̶ Scientific Articles and Journals (WoS – Scopus as seen in 2.Scientometry)
̶ Chemical and other information
̶ Specific properties and parameters
Ludovic Mayer – 3. Database6
Database: From “paper” to today
̶ First chemical database
̶ First edition published in 1817,
last edition: 8th edition 1990’s
Nowadays most of them are digitalized and the information is available online
Ludovic Mayer – 3. Database7
Chemical databases
̶ Multiple existing databases based on different criterias
̶ according to chemical structures
̶ literature
̶ crystallographic
̶ spectroscopic: infrared, absorbance, nuclear magnetic resonance, …
̶ reactions
̶ thermodynamic
̶ others, …
Ludovic Mayer – 3. Database8
Chemical databases
̶ Often based on chemical structures searches
̶ Chemical structures are easy to read by humans (visual reading, …)
̶ How to explain it to computer / software / app ?
1,5-Dihydroxy-4,8-dinitro-9,10-dioxo-9,10dihydroanthracene-2,6-disulfonic
acid
Ludovic Mayer – 3. Database9
Chemical structures and their representation
̶ In order to look for a structure and for the computer to understand
a) Name (or similar unique identifier)
b) Connectivity matrices (e.g.MDL molfile, PDB, CML, … = Computer
languages related to chemistry created specifically for computation
c) Linear strings: e.g. SMILES/SMARTS, SLN, WLN, InChi = easy
computer language which computer can decipher the structure
Ludovic Mayer – 3. Database10
Chemical name (or similar unique identifier)
̶ Each compound can have multiple names
̶ Common name (trivial, semi-trivial, systematic, business, …)
▪Chlorpyrifos (Insecticide, banned since 2020 in Europe)
̶ Proper chemical name: (= IUPAC name, International Union of Pure and Applied Chemistry)
▪0,0-diethyl 0-(3,5,6-trichloro-2-pyridinyl)-phosphorothioate
̶ Other names (sometimes names of commercial products they are featured in)
▪Chlorpyrifos-ethyl, Brodan, Bolton insecticide, Cobalt, …
Ludovic Mayer – 3. Database11
Chemical name (or similar unique identifier)
̶ In order to remove possible errors and mistakes:
̶ A unique numerical identifier was created =
̶ CAS RN (Chemical Abstracts Service Registry Number)
̶ Assigned to every chemical substance
̶ From 1800’s to today, registry account from more than 193 million
compounds
Ludovic Mayer – 3. Database12
Chemical name (or similar unique identifier)
̶ Chlorpyrifos: CAS RN = 2921-88-2
Metabolites and derivatives:
̶ Chlorpyrifos-methyl = 5598-13-0
̶ Chlorpyrifos-oxon: 5598-15-2
Ludovic Mayer – 3. Database13
Connectivity Matrix
̶ Computer language
̶ Chemical Table File (CT File)
̶ Family of text based chemical file formats that describe molecules and chemical reactions
̶ Numerous file format exist
̶ CT File is an open format
̶ Lists each atom in a molecule, with the x-y-z coordinates of that atom, and the bonds
amongst atoms
̶ Just need to register on this website to access them: https://discover.3ds.com/ctfile-
documentation-request-form
Ludovic Mayer – 3. Database14
Molfile:
̶ An MDL Molfile is a file format
̶ Contains information about:
̶ atoms,
̶ bonds, (=connectivity)
̶ charges
̶ coordinates of a molecule
̶ Recognized by most cheminformatics
software systems/applications
Connectivity Matrix
Ludovic Mayer – 3. Database15
Connectivity Matrix
̶ Same exist for Proteins = PDB format
Ludovic Mayer – 3. Database16
Connectivity Matrix without connectivity
X-Y-Z file
̶ No information about bonds (covalent,
hydrogens, VdW, …) admits a greater
flexibility
̶ Typical XYZ format specifies the molecule
geometry
̶ First line = number of atoms with Cartesian
coordinates
̶ Second line = a comment
̶ Third and following line = atomic coordinates
Ludovic Mayer – 3. Database17
Connectivity Matrix without connectivity
Pyridine
̶ Formula: C5H5N
Ludovic Mayer – 3. Database18
Linear string: SMILES
Linear string: represents structures as a linear string of characters
Simplified Molecular Input Line Entry Specification (SMILES)
̶ Chemical notation allowing user to represent a chemical structure
̶ Easily read, understood and used by computer
̶ Contains connectivity, but no longer 2D or 3D coordinates
Ludovic Mayer – 3. Database19
Linear string: SMILES
̶ How does it work?
̶ Every atoms are supported
̶ Upper-case for aromatic atoms, lowercase
for non-aromatic atoms
̶ Bonds:
– single bond
= double bond
# triple bond
* aromatic bond
. disconnected structures
Ludovic Mayer – 3. Database20
Linear string: SMILES
Simple chain molecule
(Hydrogen suppressed = no need to put hydrogen in it, software understand that they are here)
SMILES Formula Name Structure
CC CH3CH3 Ethane
C=C CH2CH2 Ethene
CBr CH3Br Bromomethane
Ludovic Mayer – 3. Database21
Linear string: SMILES
Simple chain molecule
(Hydrogen suppressed = no need to put hydrogen in it, software understand that they are here)
SMILES Formula Name Structure
CC CH3CH3 Ethane
C=C CH2CH2 Ethene
CBr CH3Br Bromomethane
Ludovic Mayer – 3. Database22
Linear string: SMILES
Branches
(in parentheses = a branche placed right after the atom it is connected to)
SMILES Formula Name Structure
CC(O)C CH3CHOHCH3 2-propanol
CC(=O)C CH3COCH3
2-propanone
(acetone)
CC(CC)C CH3CH3CHCH2CH3
2-methylbutane
(Isopentane)
Ludovic Mayer – 3. Database23
Linear string: SMILES
Branches
(in parentheses = a branche placed right after the atom it is connected to)
SMILES Formula Name Structure
CC(O)C CH3CHOHCH3 2-propanol
CC(=O)C CH3COCH3
2-propanone
(acetone)
CCC(C)C CH3CH3CHCH2CH3
2-methylbutane
(Isopentane=
Ludovic Mayer – 3. Database24
Linear string: SMILES
Rings:
(Use number to identify opening and closing of ring atom)
SMILES Formula Name Structure
C=1CCCCC1
Also
C*1*C*C*C*C*C1
CHCHCH2CH2CH2CH Cyclohexene
C1OC1CC CH2(O)CHCH2CH3 Ethyloxirane
c1cc2ccccc2cc1 CHCHCHCHCHCHCHCHCHCH Naphtalene
1
1
1
2
Ludovic Mayer – 3. Database25
Linear string: SMILES
Rings:
(Use number to identify opening and closing of ring atom)
SMILES Formula Name Structure
C=1CCCCC1
Also
C*1*C*C*C*C*C1
CHCHCH2CH2CH2CH Cyclohexene
C1OC1CC CH2(O)CHCH2CH3 Ethyloxirane
c1cc2ccccc2cc1 CHCHCHCHCHCHCHCHCHCH Naphtalene
1
1
1
2
Ludovic Mayer – 3. Database26
Linear string: SMILES
Charged atoms:
(Atoms followed by brackets which enclose the charge on the atom, maybe be
explicitly stated ({-1}) or not ({-}))
SMILES Name Structure
CCC(=O)O{-1}
Or
CCC(=O)O{-}
Ionised form of propanoic acid
c1ccccn{+1}1CC(=O)O 1-Carboxylmethyl pyridinium
Ludovic Mayer – 3. Database27
Linear string: InChI
InChI
̶ International
Chemical Identifier
̶ Introduced by IUPAC
as a standard in
2006
̶ Contains different
layers:
̶ general formula,
̶ hydrogens, charges,
̶ stereochemistry,
̶ isotopes,…
Ludovic Mayer – 3. Database28
Representation of structure - Conclusions
̶ Chemical names – connectivity matrices – linear strings
̶ Multiple choice exist, none of them wrong, some more popular than others
Ludovic Mayer – 3. Database29
Questions?
̶ Contact me anytime via email: ludovic.mayer@recetox.muni.cz