ChemSketch the most easiest thing in SBM 4021

Zanamivir (zmr)

8 structure reactions

These are the result of my ChemSketching today! Happy because I did it well. Alhamdulillah.

I use chemsketch software to make this structure.

This software can be used to draw many pictures especially used in chemistry.

You can refer to my previous lesson of this Chemsketch( Click here http://balqisandkos1110.blogspot.com/2010/10/chem-sketch.html ). It might help you to get more view on what is ChemSketch is all about. Have a nice day!

Assalamualaikum :)

BIOINFORMATIC TOOLS: I SHOULD MASTER THIS

Assalamualaikum wbt..
Today is my second class of CADD..
I supposed to enter last Tuesday class, but I was just having my wisdom tooth operation on Monday, thus I didn't come to class. Since my friend said that I should not miss this class for this week, I decided to enter the other section. Fortunately, there are a lot of section for this subject. 5 sections all.

Alright, for today class, Dr. Linda had taught us 4 bioinformatics tools.
1) BLAST
2) InterProScan
3) Catalytic Site Atlas (CAS)
4) Multiple Sequence Alignment (MSA)

BLAST

BLAST can help you to find 3 results from your sequence:
i) conserve domain
ii) graph
iii) alignment

Our PDB ID is 2HT5 (according to last class assignment)

Copy the FASTA sequence in Notepad (copy from Protein BLAST) > alter

Paste FASTA and choose PSI-BLAST for algorithm

Wait a few seconds. It is loading.
And you will get this result.

Query Seq is the sequence that we paste before, and it shows with green triange the catalytic sites.
Sialidase is the conserve domain (i) which is the other name of neuraminidase (2H5T).

Graph (ii) can be obtained by clicking on the red line.

2) InterProScan

InterProScan4 has similar function with BLAST but it is more details that you will be surprised when you found out that you actually have 2 conserved domain on your sequence!

Here the steps:

>Start with IPR

>Enter FASTA sequence (protein only)

>Submit

 
3) Catalytic Site Atlas (CAS)

CAS is a tool use basically to search active site on your sequence.
I'll expalin this on next post okay! Multiple Sequence Alignment (MSA) okay? Need to hurry. Bus is coming!

Wallahualam...:)

SBM4021

Assalamualaikum WBT

Computer Aided Drug Design Class brings me to this wall again. Heh~

Can't believe that it has been 4 years already

This was what we did today. Mesmerizing KOS1110 class back in 2010. :)

 N8 Neuraminidase
Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)

•>EMBOSS_001

•ACCTACATGAACAACACCGAGGCCATCTGCGACGCCAAGGGCTTCGCCCCCTTCAGCAAGGACAACGGCATCAGGATCGGCAGCAGGGGCCACATCTTCGTGATCAGGGAGCCCTTCGTGAGCTGCAGCCCCATCGAGTGCAGGACCTTCTTCCTGACCCAGGGCAGCCTGCTGAACGACAAGCACAGCAACGGCACCGTGAAGGACAGGAGCCCCTTCAGGACCCTGATGAGCGTGGAGGTGGGCCAGAGCCCCAACGTGTACCAGGCCAGGTTCGAGGCCGTGGCCTGGAGCGCCACCGCCTGCCACGACGGCAAGAAGTGGATGACCGTGGGCGTGACCGGCCCCGACAGCAAGGCCGTGGCCGTGATCCACTACGGCGGCGTGCCCACCGACGTGGTGAACAGCTGGGCCGGCGACATCCTGAGGACCCAGGAGAGCAGCTGCACCTGCATCCAGGGCGACTGCTACTGGGTGATGACCGACGGCCCCGCCAACAGGCAGGCCCAGTACAGGATCTACAAGGCCAACCAGGGCAGGATCATCGGCCAGACCGACATCAGCTTCAACGGCGGCCACATCGAGGAGTGCAGCTGCTACCCCAACGACGGCAAGGTGGAGTGCGTGTGCAGGGACGGCTGGACCGGCACCAACAGGCCCGTGCTGGTGATCAGCCCCGACCTGAGCTACAGGGTGGGCTACCTGTGCGCCGGCATCCCCAGCGACACCCCCAGGGGCGAGGACACCCAGTTCACCGGCAGCTGCACCAGCCCCATGGGCAACCAGGGCTACGGCGTGAAGGGCTTCGGCTTCAGGCAGGGCACCGACGTGTGGATGGGCAGGACCATCAGCAGGACCAGCAGGAGCGGCTTCGAGATCCTGAGGATCAAGAACGGCTGGACCCAGACCAGCAAGGAGCAGATCAGGAAGCAGGTGGTGGTGGACAACCTGAACTGGAGCGGCTACAGCGGCAGCTTCACCCTGCCCGTGGAGCTGAGCGGCAAGGACTGCCTGGTGCCCTGCTTCTGGGTGGAGATGATCAGGGGCAAGCCCGAGGAGAAGACCATCTGGACCAGCAGCAGCAGCATCGTGATGTGCGGCGTGGACTACGAGGTGGCCGACTGGAGCTGGCACGACGGC GCCATCCTGCCCT

•>2HT5:A|PDBID|CHAIN|SEQUENCE

•TYMNNTEAICDAKGFAPFSKDNGIRIGSRGHIFVIREPFVSCSPIECRTFFLTQGSLLNDKHSNGTVKDRSPFRTLMSVE VGQSPNVYQARFEAVAWSATACHDGKKWMTVGVTGPDSKAVAVIHYGGVPTDVVNSWAGDILRTQESSCTCIQGDCYWVMTDGPANRQAQYRIYKANQGRIIGQTDISFNGGHIEECSCYPNDGKVECVCRDGWTGTNRPVLVISPDLSYRVGYLCAGIP SDTPRGEDTQFTGSCTSPMGNQGYGVKGFGFRQGTDVWMGRTISRTSRSGFEILRIKNGWTQTSKEQIRKQVVVDNLNWS GYSGSFTLPVELSGKDCLVPCFWVEMIRGKPEEKTIWTSSSSIVMCGVDYEVADWSWHDGAILPFDIDKM

Ok..What is this?? To be continue..........

XML.."AWESOME"

Yesterday was Monday, as usual, we have Computer In Science class. Madam Linda was giving us quiz. It is about HTML, Internet, and SMILES. Alhamdulillah. I thought I was doing okay but still, I don't know my answer are exact or not. After that, Madam Linda tought us about the new topic XML which stands for Extension Markup Language. It is much like HTML but they play different roles.


XML Tree


XML Syntax



XML Table

MOLECULAR MECHANISMS	SEMI EMPIRICAL	AB INITIO
VERY FAST	FAST	SLOW
PARAMETER RESTRICTION	GOOD ACCURACY	VERY GOOD

PDB.."WONDERFUL"

Last week, i learned about PDB Protein Data Bank. I think this topics is definitely important for a biomedical science student like me.Ii believe that i m going to use this knowledge in future. I am very sorry to my lecturer, Madam Linda because i m late to post this topic. These past few weeks, the internet connection in my living area was very unconvenience for me to do the homework. Plus, i m not having an laptop as well as broadband now. Thank you madam for being so understanding.

PDB Protien Data Bank

*display:ribbon,colors:structure

*dispaly:wireframe,colors:group

This PDB images is 3LGI created by RasMol Version 2.6.

SMILES

Simplified Molecular Input Line Entry Specification(SMILES) is a specification of unambiguously describing the stucture of chemical molecules using short ASCII strings.

The table below summarised the topic that we cover in SMILES:

NO	TOPIC
1	Introduction of SMILES
2	SMILES Bonds
3	SMILES Branches
4	SMILES Atoms
5	SMILES Charges
6	SMILES Cyclic Structures
7	SMILES Conventions and Restrictions
8	SMILES Fragments
9	SMILES Metals

Tutorials:

1)

2)

3)

4)

Last but not least, who are interested to know more about SMILES, you can get SMILESCAS Database by clicking here.

Thank you.

Microsoft Excel.."NOW I KNOW"

Assalamualaikum..today, in KOS class..we learned about how to use Microsoft Excel. It was enjoyable but yet, we all know the fact that technology is sometimes against us. Maybe it was due to my lackness of knowledge about computer since i have never took any computer class before. Too bad! By using Microsoft Excel, we can organize the data in rows and column. Then, we can use it to perform mathematics calculations quickly such as graphs.

For today's duty, we should solve the tutorial that had been given by Madam Linda through my e-mail.

Part 1	Beer's Law Plot
Part 2	Titration
Tutorial 1	the percentage injured p against the temperature
Tutorial 2	the number of new housing starts per year

Part 1

Part 2

Tutorial 1

Tutorial 2