Extensible Markup Language (XML)

XML- Extensible Markup Language

- was designed to describe data and focus what data is.
- XML's design goals emphasize simplicity, generality, and usability over the internet.
- Although the design of XML focuses on documents, it is widely used for the representation of arbitrary data structures, for example in web services.
- is a markup language much like HTML.
- tags are not predefined.

1) XML syntax



2) XML tree




3) XML table

Computational method:

Method	Molecular mechanics	Semi empirical	Ab initio
Speed	Very fast speed	Fast speed	Slow speed
Accuracy	Parameter restriction	Good accuracy	Very good accuracy

PDB-PROTEIN DATA BANK

PDB- The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.

- The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

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

example of pdb:



thank you...happy PDB-ing... ;))))

SMILES

SMILES- simplified molecular input line entry system

Tutorial 1:


tutorial 2:

tutorial 3:




thank you..SMILES SOKMO dehh... :)

EXCEL (REGRESSION)

1) Beer's law plot data

2) Titration of 50 mL of 0.1 M HCl with 0.1 M NaOH
3) Percentage of runners injured in Boston Marathon


4) No. of new housing starts (in thousand) for 1990 through 1997

thank you..regress your head straight! ;)))

|CHEMSKETCH|

what is chemsketch?
chemsketch is a commonly used chemical drawing program for 2D and 3D structures, copyright of Advanced Chemistry Development, Inc. The program has certain additional features including calculation of molecular weight, calculation of percentages of elements present, IUPAC name generation, and viewing in RasMol.

here are some of the "sketch-es" or drawing made during the previous class.





thank you..sketch yourself now! ;D