EXCEL

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.







Linear regression

Introduction to linear regression
Linear regression analyzes the relationship between two variables, X and Y. For each subject (or experimental unit), you know both X and Y and you want to find the best straight line through the data. In some situations, the slope and/or intercept have a scientific meaning. In other cases, you use the linear regression line as a standard curve to find new values of X from Y, or Y from X.
The term "regression", like many statistical terms, is used in statistics quite differently than it is used in other contexts. The method was first used to examine the relationship between the heights of fathers and sons. The two were related, of course, but the slope is less than 1.0. A tall father tended to have sons shorter than himself; a short father tended to have sons taller than himself. The height of sons regressed to the mean. The term "regression" is now used for many sorts of curve fitting.
Prism determines and graphs the best-fit linear regression line, optionally including a 95% confidence interval or 95% prediction interval bands. You may also force the line through a particular point (usually the origin), calculate residuals, calculate a runs test, or compare the slopes and intercepts of two or more regression lines.
In general, the goal of linear regression is to find the line that best predicts Y from X. Linear regression does this by finding the line that minimizes the sum of the squares of the vertical distances of the points from the line.
Note that linear regression does not test whether your data are linear (except via the runs test). It assumes that your data are linear, and finds the slope and intercept that make a straight line best fit your data.

Quadratic Regression is a process by which the equation of a parabola is found that “best fits” a given set of data.Quadratic regression models are often used in economics areas such as utility function, forecasting, cost-befit analysis.

Beer`s law plot data

Titration

answer for question 1

answer for question 2

http://www.graphpad.com/curvefit/linear_regression.htm 

http://en.wikipedia.org/wiki/Microsoft_Excel

SMILES :)

What`s that????

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).

Here are some of the images that I had done on this topic;

http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
http://en.wikipedia.org/wiki/Smile

protein data bank

WHAT is PDB???

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.^[1]

HISTORY...

The PDB originated as a grassroots effort.^[1] In 1971, Walter Hamilton of the Brookhaven National Laboratory agreed to set up the data bank at Brookhaven. Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB. In January 1994, Joel Sussman was appointed head of the PDB. In October 1998,^[2] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the member institutions of the RCSB).^[3] In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB(USA), andPDBj (Japan). The BMRB joined in 2006. Each of the four members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotates each submitted entry. The data are then automatically checked for plausibility. (The source code for this validation software has been made available to the public at no charge.

FTSH peptidase...

image of ftsh peptidase

Author	Tomaras, A.P.,
Experiment	X-RAY DIFFRACTION with resolution of 2.00 Å
Chain	A
EC	3.6.5.4

Gene Ontology

Cellular component	protein complex (GO:0043234)
Biological process	protein polymerization (GO:0051258)

THERMOLYSIN...

image of termolysin

Author	Senda, M.,   Senda, T.,   Kidokoro, S.
Experiment	X-RAY DIFFRACTION with resolution of 1.70 Å
Chain	A
EC	3.4.24.27

Gene Ontology

Cellular component	extracellular region (GO:0005576)
Molecular function	metalloendopeptidase activity (GO:0004222)
Biological process	proteolysis (GO:0006508)

LEUCYL AMINOPEPTIDASE...

image of leucyl aminopeptidase

Author	Kale, A.,   Dijkstra, B.W.,   Sonke, T.,
Experiment	X-RAY DIFFRACTION with resolution of 1.50 Å
Chain	A, B, C, D, E, F
EC	3.4.24.27

Gene Ontology

Cellular component	intracellular (GO:0005622)
Molecular function	aminopeptidase activity (GO:0004177)
Biological process	proteolysis (GO:0006508)

http://www.rcsb.org/pdb/home/home.do

http://en.wikipedia.org/wiki/Protein_Data_Bank

http://www.genome.jp/kegg/pathway.html