..::Excel::..

 

Microsoft Excel is a commercial spreadsheet application written and distributed by Microsoft for Microsoft Windows and Mac OS X. It features calculation, graphing tools, pivot tables and a macro programming language called Visual Basic for Applications. It has been a very widely applied spreadsheet for these platforms, especially since version 5 in 1993. Excel forms part of Microsoft Office. The current versions are 2010 for Windows and 2011 for Mac.

 

SCATTER PLOT IN EXCEL

Objectives:

• Enter and format data in an Excel spreadsheet in a form appropriate for graphing
• Create a scatter plot from spreadsheet data
• Insert a linear regression line (trendline) into the scatter plot
• Use the slope/intercept formula for the regression line to calculate a x value for a known y value
• Explore curve fitting to scatterplot data
• Create a connected point (line) graph
• Place a reference line in a graph

 

SCATTER PLOT IN EXCEL

Objectives

• Enter and format data in an Excel spreadsheet in a form appropriate for graphing
• Create a scatter plot from spreadsheet data
• Insert a linear regression line (trendline) into the scatter plot
• Use the slope/intercept formula for the regression line to calculate a x value for a known y value
• Explore curve fitting to scatterplot data
• Create a connected point (line) graph
• Place a reference line in a graph

Introduction Beer's Law states that there is a linear relationship between concentration of a colored compound in solution and the light absorption of the solution. This fact can be used to calculate the concentration of unknown solutions, given their absorption readings. First, a series of solutions of known concentration are tested for their absorption level. Next, a scatter plot is made of this empirical data and a linear regression line is fitted to the data. This regression line can be expressed as a formula and used to calculate the concentration of unknown solutions.

Part 1 - Beer's Law Scatter Plot and Linear Regression

This was the graph that I did:>

Next graph is about Titration Data.Lets look at it

Part 2 - Titration Data Plotting

Creating a Scatter Plot of Titration Data

In this next part of the tutorial, we will work with another set of data. In this case, it is of a strong acid-strong base titration. With this titration, a strong base (NaOH) of known concentration is added to a strong acid (also of known concentration, in this case). As the strong base is added to solution, its OH- ions bind with the free H+ions of the acid. An equivalence point is reached when there are no free OH- nor H+ ions in the solution. This equivalence point can be found with a color indicator in the solution or through a pH titration curve. This part of the tutorial will show you how to do the latter. 

This was the graph that I had plot:>

There are two of it altogether.One with non-gridlines and the other one with the gridliness....   

Part 3 : Finding the line of best fit

The table shows the temperature at the start of the race and the percentage of runners injured in eight running of the Boston Marathon.

These are the graph detailed about Boston Maratahon

 

Part 4 :  Quadratic regression

The following table shows the number of new housing starts (in thousand) for 1990 through 1997.

 And this was the graph related to it....>

After all,thanks a lot Madam...may Allah bless you n your family.....=)

.::: SMILES :::.

Alhamdulillah, this week, we got an assingment title "SMILE".At first, I thought it is a task to draw smiley faces by using chemsketch but I got it wrong.....=)  

"SMILES"  refer to Simplified Molecular Input Line Entry Specification

SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.

Lets look at its explanation below:>

SMILES contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. SMILES is a true language, albeit with a simple vocabulary (atom and bond symbols) and only a few grammar rules. SMILES representations of structure can in turn be used as "words" in the vocabulary of other languages designed for storage of chemical information (information about chemicals) and chemical intelligence (information about chemistry).

Part of the power of SMILES is that unique SMILES exist. With standard SMILES, the name of a molecule is synonymous with its structure; with unique SMILES, the name is universal. Anyone in the world who uses unique SMILES to name a molecule will choose the exact same name.

One other important property of SMILES is that it is quite compact compared to most other methods of representing structure. A typical SMILES will take 50% to 70% less space than an equivalent connection table, even binary connection tables. For example, a database of 23,137 structures, with an average of 20 atoms per structure, uses only 1.6 bytes per atom when represented with SMILES. In addition, ordinary compression of SMILES is extremely effective. The same database cited above was reduced to 27% of its original size by Ziv-Lempel compression (i.e. 0.42 bytes per atom).

These properties open many doors to the chemical information programmer. Examples of uses for SMILES are:

• Keys for database access
• Mechanism for researchers to exchange chemical information
• Entry system for chemical data
• Part of languages for artificial intelligence or expert systems in chemistry

The rest of this chapter is a concise exposition of the SMILES encoding rules. For further information, the reader is referred to "SMILES 1. Introduction and Encoding Rules", Weininger, D., J.Chem. Inf. Comput. Sci. 1988, 28,31. 

You can further learn this interesting application by clicking this link:

http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

There are four tasks altogether.It is not that easy for those who never experience using chemsketch application. But you can try right??..."No works and no play makes Jack a dull boy"You will feel it is quite an interesting application as you will find it easy at the end.....=)...

Lets look at my workarts that I did in the lab on Wednesday,12 January 2011:

First slide: I was blurred at first....hehe3x

Second slide : ....hmm my feeling of excitement developed slowly....(^_^)\

Third slide: I become eagerly excited to finish it!....[^,^]v

Fourth slide:...Alhamdulillah....all praises be to Him...I achieved my goal!!!!

Thats all from the humble me...See you next time!!!

Special thanks to Madam Linda for her guide.....Thanks a lot Madam!! =)

..::Protein Data Bank (PDB)::..

Next Chapter, we will introduce you about PDB:>

  PROTEIN DATA BANK (PDB)

PDB - an introduction to a common term

» What is PDB?

1-The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules.

2- A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections: (i) a header that contains much background information on the molecule in question such as authors and experimental conditions, (ii) 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.

>>How can PDB's be visualized?

Protein Data Bank files, containing some form of macromolecular coordinate set, are visualized via graphic computing. A myriad of advanced molecular visualization programs are used in academic and industrial setting, and some of these are specific to the field of research or the techniques used to collect the coordinate data. For example, X-ray crystallographers use O, XtalView, MAIN, or other programs for crystallographic modeling. These allow the researcher to model the coordinate set into the electron density from the collected X-ray data.
However, PDB files are "final" deposited coordinates. This means that the depositor has made their best effort to provide a final model that is as accurate as they could make it. Programs like Molscript, Pymol, SwissPDBview/DeepView, Molmol, SETOR, DINO and others are routinely used to visualize deposited coordinates.
In order to produce molecular graphics, one requires the following: graphics workstation computer, some form of molecular graphics software, and most importantly, training.
Symmation has been formally trained in X-ray crystallography and bioinformatics. We have the software and computer equipment, aside from our 8 years of experience. We are able to provide a complete solution to molecular graphics visualization that includes raw data interpretation, remodeling, refinement, structure analysis, and of course publication-quality graphics.
We can reduce your costs of operation, whatever sector you are in. Request information on PDB visualization and read our client testimonials that speak on our expertise!

 You may look at these three example below /(^_^)\ >

• Subtilisin
• Prolyl Aminopeptidase
• Lex A Repressor

Lets look at it,Jom!!

Subtilisin

The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.

The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) X-ray structure of a complex formed between trypsin and a canonical inhibitor acting... [ Read More & Search PubMed Abstracts ]
The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) X-ray structure of a complex formed between trypsin and a canonical inhibitor acting through a substrate-like mechanism. The electron density indicates the protonation state of all catalytic residues where the catalytic histidine is, as expected, in its neutral state prior to the acylation step by the catalytic serine. The carboxyl group of the catalytic aspartate displays an asymmetric electron density so that O?2-C? bond appears to be a double bond, with O?2 involved in a hydrogen bond to His-57 and Ser-214. Only when Asp-102 is protonated on O?1 atom a DFT simulation could reproduce the observed electron density. The presence of a putative hydrogen atom is also confirmed by a residual mFobs-DFcalc density above 2.5 ? next to O?1. As a possible functional role for the neutral aspartate in the active site, we propose that in the substrate bound form the neutral aspartate residue helps to keep the pKa of the histidine sufficiently low, in the active neutral form. When the histidine receives a proton during the catalytic cycle, the aspartate becomes simultaneously negatively charged providing additional stabilization for the protonated histidine and indirectly to the tetrahedral intermediate. This novel proposal unifies the seemingly conflicting experimental observations, which were previously seen as either supporting the charge relay mechanism or the neutral-pKa histidine theory.

Prolyl peptidase

The structural basis for catalysis and specificity of the X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis.

Rigolet, P.,   Mechin, I.,   Delage, M.M.,   Chich, J.F.

PubMed Abstract:
The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for... [ Read More & Search PubMed Abstracts ]
The X-prolyl dipeptidyl aminopeptidase (X-PDAP) from Lactococcus lactis is a dimeric enzyme catalyzing the removal of Xaa-Pro dipeptides from the N terminus of peptides. The structure of the enzyme was solved at 2.2 A resolution and provides a model for the peptidase family S15. Each monomer is composed of four domains. The larger one presents an alpha/beta hydrolase fold and comprises the active site serine. The specificity pocket is mainly built by residues from a small helical domain which is, together with the N-terminal domain, essential for dimerization. A C-terminal moiety probably plays a role in the tropism of X-PDAP toward the cellular membrane. These results give new insights for further exploration of the role of the enzymes of the SC clan.

 

Lex A Repressor

Repressor LexA or LexA is a repressor enzymeEC 3.4.21.88) that represses SOS response genesDNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a process called autoproteolysis. ( coding for

DNA damage can be inflicted by the action of antibiotics. Bacteria require topoisomerases such as DNA gyrase or topoisomerase IV for DNA replication. Antibiotics such as ciprofloxacin are able to prevent the action of these molecules by attaching themselves to the gyrase - DNA complex. This is counteracted by the polymerase repair molecules from the SOS response. Unfortunately the action is partly counterproductive because ciprofloxacin is also involved in the synthetic pathway to RecA type molecules which means that the bacteria responds to an antibiotic by starting to produce more repair proteins. These repair proteins can lead to eventual benevolent mutations which can render the bacteria resistant to ciprofloxacin.

Mutations are traditionally thought of as happening as a random process and as a liability to the organism. Many strategies exist in a cell to curb the rate of mutations. Mutations on the other hand can also be part of a survival strategy. For the bacteria under attack from an antibiotic, mutations help to develop the right biochemistry needed for defense. Certain polymerases in the SOS pathway are error-prone in their copying of DNA which leads to mutations. While these mutations are often lethal to the cell, they can also lead to mutations which improve the bacteria's survival. In the specific case of topoisomerases, some bacteria have mutated one of their amino acids so that the ciproflaxin can only create a weak bond to the topoisomerase. This is one of the methods that bacteria use to become resistant to antibiotics.

Impaired LexA proteolysis has been shown to interfere with ciprofloxacin resistance.This offers potential for combination therapy that combine quinolones with strategies aimed at interfering with the action of LexA either directly, or via RecA.

That's all from helpless me.Do comment if you like to..=)

..::Chem Sketch::..

~Welcome to Chem Sketch world~

Creating Graphical Objects

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.

This chapter will familiarize you with the creation of graphical objects. Switch to the Draw mode before proceeding with any exercise in this chapter.

You will learn how to use Draw mode tools for creating the following objects:

• A diagram of the energy of reaction

•Various types of orbitals

•Vacuum distillation apparatus

•A two-chain DNA strand

•Lipids and micelles

Drawing the Energy of Reaction Diagram

Drawing Different Kinds of Orbitals

Drawing Vacuum Distillation Apparatus

Drawing a Two-chain DNA Strand

Drawing Lipids and Micelles

For more information, you can just click the link below /(^_^)\:

http://www.acdlabs.com/download/chemsketch/

Name	Date	Download
ChemSketch Freeware(including CD/log/Freeware and ChemBasic,	2010-06-30	Download
ACD/NMR Processor Academic Edition	2010-03-18	Download
ACD/Column Selector	2010-02-24	Download