Monday, October 18, 2010

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:

MethodMolecular mechanicsSemi empiricalAb initio
SpeedVery fast speedFast speedSlow speed
AccuracyParameter restrictionGood accuracyVery good accuracy

Monday, October 11, 2010


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.


example of pdb:

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


SMILES- simplified molecular input line entry system

Tutorial 1:

tutorial 2:

tutorial 3:

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

Sunday, October 10, 2010


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! ;)))


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