Fix Komputasi Annita

8/11/2019 Fix Komputasi Annita

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1) Find three bad or evil databases in the biochemistry/chemistry world please give a reason

in a short sentence.

Answer:

A.

http://webbook.nist.gov/chemistry/

Alasan singkat:

1.

Tidak terdapat kotak pencarian (query)2. Hanya terdiri dari list-list sehingga menyulitkan pencarian

B. http://www.chemnetbase.com/
http://webbook.nist.gov/chemistry/http://webbook.nist.gov/chemistry/http://www.chemnetbase.com/http://www.chemnetbase.com/http://www.chemnetbase.com/http://webbook.nist.gov/chemistry/


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Alasannya singkat:

1. Tidak terdapat kotak pencarian (query)

2. Hanya terdiri dari list-list sehingga menyulitkan pencarian

3. Terdapat link list yang tidak dapat diakses karena harus memiliki aplikasi

untuk membukanya. Misalkan:


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4. Terdapat link yang apabila dibuka diharuskan untuk log in sebelum akses

halaman tersebut. Misalkan :

C. http://www.martindalecenter.com/Reference_3_Chemicals.html

Alasan singkat:

1. Tidak terdapat kotak pencarian sehingga sulit untuk mencari data yang

diinginkan

2. Datanya tidak lengkap dan tidak begitu akurat

2) Find the year in which most papers about enzyme kinetics were published using

PubMed (use Explore enter search term, then Analyze year)

Answer :
http://www.martindalecenter.com/Reference_3_Chemicals.htmlhttp://www.martindalecenter.com/Reference_3_Chemicals.htmlhttp://www.martindalecenter.com/Reference_3_Chemicals.html


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Paper mengenai enzim kinetik yang dipublikasi menggunakan PubMed paling banyak

terdapat pada tahun 2002 sebanyak 7981 items.

3)

Find the molecules which were analyzed most in papers regarding "enzyme kinetics" and"crickets using PubChem (use Explore, then Analyze CAS Number)

Answer :

4) Find the price for 1g ATP from Pfaltz & Bauer (in SciFinder use locate substance then

use the Erlenmeyer icon for price info)

Answer:

1g ATP from Pfaltz & Bauer = ADENOSINE 5-TRIPHOSPHATE , 1G ADENOSINE 5-TRIPHOSPHATE , 1G Adenosine 5-Triphosphate Disodium Salt CAS: 987-65-5. The

Price is $89.95.

5) GotoBrenda and find out how many coronavirus types are in the DB (use TaxExplorer

and query)

Answer:

Disimpulkan terdapat 11 tipe coronavirus dalam database Brenda, antara lain:

a) Alphacoronavirus.

b) Human coronavirus.

c) SARS coronavirus Urbani.

d) Bovine coronavirus.

e) Feline coronavirus.
http://www.neobits.com/_p3314457.html?referrer=catchphttp://www.brenda-enzymes.info/http://www.brenda-enzymes.info/http://www.neobits.com/_p3314457.html?referrer=catchp


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f) Murine coronavirus.

g) Puffinosis coronavirus.

h) Rat sialodacryoadenitis coronavirus.

i) Betacoronavirus.

j) Unidentifield human coronavirus

k) Alphacoronavirus SARS

Berikut ini adalah screenshot tipe organisme dari coronavirus


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6) Goto Brenda and find out how many enzymes are listed as resistant against

perchloric acid, report publication title (goto Brenda, Advanced search)!

Answer:

Results 1- 10of 14

EC NUMBER RECOMMENDE

D NAME

SYNONYMS COMME

NTARY

1.1.1.37 malate

dehydrogenase

NAD+-MDH enzymes -

1.8.2.2 thiosulfatedehydrogenase

enzymes, thiosulfate-oxidizing

-

1.14.15.6 cholesterol

monooxygenase

(side-chain-

cleaving)

endoenzymes, cholesterol

side-chain-cleaving

-
http://www.brenda-enzymes.info/http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.1.1.37http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.1.1.37http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.8.2.2http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.8.2.2http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=1.14.15.6http://openreactionwindow%28%271.14.15.6%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=1.8.2.2http://openreactionwindow%28%271.8.2.2%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=1.1.1.37http://openreactionwindow%28%271.1.1.37%27%29/http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.8.2.2http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.1.1.37http://www.brenda-enzymes.info/


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1.14.15.6 cholesterol

monooxygenase

(side-chain-

cleaving)

enzymes, cholesterol side-

chain-cleaving

-

2.3.1.97 glycylpeptide N-tetradecanoyltrans

ferase

myristoylating enzymes -

2.4.1.18 1,4-alpha-glucan

branching

enzyme

starch-branching enzymes IIa -

2.4.1.18 1,4-alpha-glucan

branching

enzyme

starch-branching enzymes

IIb

-

2.7.7.30 fucose-1-

phosphate

guanylyltransfera

se

GDP-L-fucose-synthesizing

enzymes

-

3.1.1.73 feruloyl esterase hemicellulase acessory

enzymes

-

3.1.22.4 crossover

junctionendodeoxyribonu

clease

Holliday junction-resolving

enzymes

-

EC Number Commentary

-3.2.2.24 ADP-ribosyl-

[dinitrogen

reductase]

hydrolase

azoferredoxin-

activating enzymes

3.4.21.95 Snake venom

factor V activator

FV activating

enzymes

3.4.21.95 Snake venom

factor V activator

Human blood

coagulation Factor

V activating
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.3.1.97http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.3.1.97http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.7.7.30http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.7.7.30http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.1.73http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.1.73http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.22.4http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.22.4http://www.brenda-enzymes.org/php/search_result.php4?a=9&RN=&RNV=1&os=&pt=&FNV=&tt=&SYN=&Textmining=&T%5b0%5d=1&W%5b1%5d=&T%5b1%5d=1&W%5b2%5d=enzymes&T%5b2%5d=2&l=10,10&orderByHTMLField=EC+Numberhttp://www.brenda-enzymes.org/php/search_result.php4?a=9&RN=&RNV=1&os=&pt=&FNV=&tt=&SYN=&Textmining=&T%5b0%5d=1&W%5b1%5d=&T%5b1%5d=1&W%5b2%5d=enzymes&T%5b2%5d=2&l=10,10&orderByHTMLField=Commentaryhttp://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.2.2.24http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.2.2.24http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=3.4.21.95http://openreactionwindow%28%273.4.21.95%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=3.4.21.95http://openreactionwindow%28%273.4.21.95%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=3.2.2.24http://openreactionwindow%28%273.2.2.24%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=3.1.22.4http://openreactionwindow%28%273.1.22.4%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=3.1.1.73http://openreactionwindow%28%273.1.1.73%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=2.7.7.30http://openreactionwindow%28%272.7.7.30%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=2.4.1.18http://openreactionwindow%28%272.4.1.18%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=2.4.1.18http://openreactionwindow%28%272.4.1.18%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=2.3.1.97http://openreactionwindow%28%272.3.1.97%27%29/http://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=1.14.15.6http://openreactionwindow%28%271.14.15.6%27%29/http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.4.21.95http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.2.2.24http://www.brenda-enzymes.org/php/search_result.php4?a=9&RN=&RNV=1&os=&pt=&FNV=&tt=&SYN=&Textmining=&T%5b0%5d=1&W%5b1%5d=&T%5b1%5d=1&W%5b2%5d=enzymes&T%5b2%5d=2&l=10,10&orderByHTMLField=Commentaryhttp://www.brenda-enzymes.org/php/search_result.php4?a=9&RN=&RNV=1&os=&pt=&FNV=&tt=&SYN=&Textmining=&T%5b0%5d=1&W%5b1%5d=&T%5b1%5d=1&W%5b2%5d=enzymes&T%5b2%5d=2&l=10,10&orderByHTMLField=EC+Numberhttp://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.22.4http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.1.73http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.7.7.30http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.4.1.18http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.3.1.97http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.14.15.6


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enzymes

5.5.1.1 Muconate

cycloisomerase

Enzymes,

muconate-

lactonizing

7)

GotoKEGG Ligand DB find the KEGG Numbers for D-Hexose and ATP

Answer:

KEGG IDs untuk D-Hexose yaitu C00738.

KEGG IDs untuk ATP yaitu C00002.
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=5.5.1.1http://www.brenda-enzymes.org/php/result_flat.php4?ecno=5.5.1.1http://www.genome.jp/kegg/ligand.htmlhttp://www.brenda-enzymes.org/sequences/index.php4?f[stype_ec]=1&second_try=1&f[ec]=5.5.1.1http://openreactionwindow%28%275.5.1.1%27%29/http://www.genome.jp/kegg/ligand.htmlhttp://www.genome.jp/kegg/ligand.htmlhttp://www.genome.jp/kegg/ligand.htmlhttp://www.brenda-enzymes.org/php/result_flat.php4?ecno=5.5.1.1


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8) GotoKEGG Reaction Prediction (e-zyme) : How many similar reactions occur between

D-Hexose and ATP? (Enter above KEGG IDs, press view structures; press compute)

Answer:
http://www.genome.jp/kegg/ligand.htmlhttp://www.genome.jp/kegg/ligand.html


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11/13

9) Goto PubChem; What is the PubChem compound ID (CID) and the topological surface

area for Tobias acid?

Answer:

The Compound ID (CID) OF Tobias Acid in PubChem database is CID 6670


12/13

Gambar berikut ini merupakan asam tobias dengan efek 3D


13/13

The topological surface area for Tobias acid is 88,8

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Fix Komputasi Annita