Baze de date utilizate in studiul bioinformatic al nucleotidelor

Chemical Entities of Biological Interest, also known as ChEBI,

https://www.ebi.ac.uk/chebi/

ChEBI, este o bază de date și ontologie a entităților moleculare axate pe compuși chimici „mici”, care face parte din
efortul Open Biomedical Ontologies. Termenul "entitate moleculară" se referă la orice "atom, moleculă, ionic,
pereche ionică, radical, ion radical, complex, conform, etc., identificabil ca o entitate distinctă separată".

ChEMBL, ChEMBLdb ,Chemspider

https://www.ebi.ac.uk/chembl/

este o bază de date chimică - molecule bioactive cu proprietăți asemănătoare medicamentului. Este
sustinut de Institutul European de Bioinformatică (EBI), al Laboratorului European de Biologie Moleculară
(EMBL), cu sediul la Wellcome Trust Genome Campus, Hinxton, Marea Britanie.
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.
http://www.chemspider.com/ https://www.youtube.com/watch?v=lST-yMe322Y
https://www.ebi.ac.uk/training/online/course/chembl-walkthrough-webinar
https://www.schrodinger.com/training/videos/small-molecule-drug-discovery/introduction-drugs-drug-targets-and-mol
ecular
FISIERE STRUCTURALE UTILE IN BIOINFORMATICA SI CHEMINFORMATICA
drug design files

1. "SMILES“ simplified molecular-input line-entry system (SMILES)

is a specification in form of a line notation for describing the structure of chemical

species using short ASCII (American Standard Code for Information
Interchange) strings. smiles strings can be imported by most molecule editors for
conversion back into two-dimensional drawings or three-dimensional models of the
molecules.

SMILES Cc1c[nH]c(=O)[nH]c1=O

PUBCHEM CC1=CNC(=O)NC1=O

http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
adenine C1=NC2=NC=NC(=C2N1)N

cytosine c1cnc(=O)[nH]c1N

Thymine Cc1c[nH]c(=O)[nH]c1=O
Unde gasim aceste fisiere-

Orice baza de data bioinformatica care prezinta informatii structurale a compusilor

chimici cu masa moleculara relativ mica

-nucleotide, AA, medicamente, etc

Complexitatea fisierului depinde de complexitatea structurala

De ce sunt utile aceste fisiere-

-permite evaluarea diferitelor proprietati farmacologice, functionala in cazul in care sunt

accesate BD care solicita acest tip de fisier

-permite modelarea moleculara a compusilor chimici prin rularea de softuri moleculare

-ex. Softul Molinspiration

-Ex Expasy –
-Softuri comerciale
 2. Molfile
-Fisier text

- stochează informații despre atomi și legături, conectivitatea și coordonatele unei molecule .

Molfile este un fisier usual in bioinformatica,

majoritatea, dacă nu toate, bazele de date / aplicațiile software cheminformatice sunt capabile
să citească formatul

Ex. ChemBl, Chemspider, etc

SciTegic01111613442D

9 9 0 0 0 0 999 V2000
1.2990 -0.7500 0.0000 N 0 0
1.2990 0.7500 0.0000 C 0 0
2.3383 1.3500 0.0000 O 0 0
0.0000 1.5000 0.0000 N 0 0
-1.2990 0.7500 0.0000 C 0 0
-2.3383 1.3500 0.0000 O 0 0
-1.2990 -0.7500 0.0000 C 0 0
-2.3383 -1.3500 0.0000 C 0 0
0.0000 -1.5000 0.0000 C 0 0
2 1 1 0 Header
9 1 1 0
2 3 2 0 Molecule name
2 4 1 0
5 4 1 0 Connection table (Ctab)
5 6 2 0 Counts line: 9 atoms, 9 bonds
5 7 1 0
Atom block (1 line for each atom): x, y, z (in angstroms),
7 8 1 0
element, etc.
7 9 2 0
M END Bond block (1 line for each bond): 1st atom, 2nd atom,
type, etc.
 3. SDF
SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural
information. "SDF" stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format.
Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). A feature of the SDF format is its
ability to include associated data

Multiple-lines data items are also supported. The MDL SDF-format specification requires that a hard-carriage-
return character be inserted if a single line of any text field exceeds 200 characters. This requirement is
frequently violated in practice, as many SMILES and InChI strings exceed that length.