Protein Data Bank + Rosmol

PROTEIN DATA BANK (PDB)

Introduction 

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. 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, 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.

RASMOL

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration ofbiological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.

Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.

RasMol has a complex version history. Starting with the series of 2.7 versions  , RasMol is licensed under a dual license (GPL or custom license RASLIC).

RasMol includes a language (for selecting certain protein chains, or changing colors etc.). Jmol and Sirius has incorporated the RasMol scripting language into its commands.

Protein Databank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography, NMR spectroscopy orelectron microscopy.

for more information about rasmol you can click here 

No.	Name	Structure	Description
1	Renin		We have found that both enantiomeric configurations of the 6-alkoxymethyl-1-aryl-2-piperazinone scaffold display equipotent renin inhibition activity and similar SAR patterns. This enantiomeric flexibility is in contrast to a previously reported 3-alkoxymethyl-4-arylpiperidine scaffold....
2	Htr A		Serine protease that cleaves beta-casein/CSN2 as well as several extracellular matrix (ECM) proteoglycans such as decorin/DCN, biglycan/BGN and fibronectin/FN1. Inhibits signaling mediated by TGF-beta family proteins possibly indirectly by degradation of these ECM proteoglycans (By similarity). May act as a tumor suppressor. Negatively regulates, in vitro, trophoblast invasion during placental development and may be involved in the development of the placenta in vivo. May also have a role in ovarian development, granulosa cell differentiation and luteinization.
3	Subtilisin		The amino acid composition of subtilisin Novo has been determined. The compositions of all of the 14 expected tryptic peptides from subtilisin Novo were obtained or deduced. A total of 281 residues was found by analysis of the protein, in good agreement with the total of 275 residues in the expected 14 tryptic peptides. The amino acid compositions and peptide maps of the tryptic peptides from subtilisin Novo and subtilisin BPN' were identical. It is concluded that the proteins are probably identical.
4	DegQ		DegQ could degrade transiently denatured and unfolded proteins which accumulate in the periplasm following stress conditions. DegQ is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for a beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable to be cleaved, thereby preventing non-specific proteolysis of folded proteins. DegQ can substitute for the periplasmic protease DegP.
5	thermolysin		Thermolysin (EC 3.4.24.27, Bacillus thermoproteolyticus neutral proteinase, thermoase, thermoase Y10, TLN) is a thermostable neutralmetalloproteinase enzyme produced by the Gram-positive bacteria Bacillus thermoproteolyticus. It requires one zinc ion for enzyme activity and four calcium ions for structural stability. Thermolysin specifically catalyzes the hydrolysis of peptide bonds containing hydrophobic amino acids. However thermolysin is also widely used for peptide bond formation through the reverse reaction of hydrolysis. Thermolysin is the most stable member of a family of metalloproteinases produced by various Bacillus species. These enzymes are also termed 'neutral' proteinases or thermolysin -like proteinases (TLPs).

internet

internet from nothing???

last two weeks we learn about the internet in class..we learn many things that we didn't know about internet.Many of the internet user take internet for granted only.Graph below show the internet host from year 1981 to 2012:

what is internet

The history of the Internet begins with the development of electronic computers in the 1950s. Initial concepts of packet networking originated in several computer science laboratories in the United States, Great Britain, and France. The US Department of Defense awarded contracts as early as the 1960s for packet network systems, including the development of the ARPANET (which would become the first network to use the Internet Protocol.) The first message was sent over the ARPANET from computer science Professor Leonard Kleinrock's laboratory at University of California, Los Angeles (UCLA) to the second network node at Stanford Research Institute(SRI).

Packet switching networks such as ARPANET, Mark I at NPL in the UK,CYCLADES, Merit Network, Tymnet, and Telenet, were developed in the late 1960s and early 1970s using a variety of communications protocols. The ARPANET in particular led to the development of protocols for internetworking, in which multiple separate networks could be joined into a network of networks.

Access to the ARPANET was expanded in 1981 when the National Science Foundation (NSF) funded the Computer Science Network (CSNET). In 1982, the Internet protocol suite (TCP/IP) was introduced as the standard networking protocol on the ARPANET. In the early 1980s the NSF funded the establishment for national supercomputing centers at several universities, and provided interconnectivity in 1986 with the NSFNET project, which also created network access to the supercomputer sites in the United States from research and education organizations. Commercial Internet service providers(ISPs) began to emerge in the late 1980s. The ARPANET was decommissioned in 1990. Private connections to the Internet by commercial entities became widespread quickly, and the NSFNET was decommissioned in 1995, removing the last restrictions on the use of the Internet to carry commercial traffic.

Since the mid-1990s, the Internet has had a revolutionary impact on culture and commerce, including the rise of near-instant communication by electronic mail, instant messaging, voice over Internet Protocol (VoIP) telephone calls,two-way interactive video calls, and the World Wide Web with its discussion forums, blogs, social networking, and online shopping sites. The research and education community continues to develop and use advanced networks such as NSF's very high speed Backbone Network Service (vBNS), Internet2, and National LambdaRail. Increasing amounts of data are transmitted at higher and higher speeds over fiber optic networks operating at 1-Gbit/s, 10-Gbit/s, or more. The Internet's takeover of the global communication landscape was almost instant in historical terms: it only communicated 1% of the information flowing through two-way telecommunications networks in the year 1993, already 51% by 2000, and more than 97% of the telecommunicated information by 2007. Today the Internet continues to grow, driven by ever greater amounts of online information, commerce, entertainment, and social networking
for more knowledge about the internet 

advantages and disadvantages of the internet

advantages	disadvantages
faster communications information resources social networking online services	theft of personal information virus threat pornography social disconnected