XML

 

Extensible Markup Language (XML) is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification^[4] produced by the W3C, and several other related specifications, all gratis open standards.^[5]
XML's design goals emphasize simplicity, generality, and usability over the Internet.^[6] It is a textual data format with strong support via Unicode for the languages of the world. Although the design of XML focuses on documents, it is widely used for the representation of arbitrary data structures, for example in web services.

 XML TABLES

TABLE OF COMPUTATIONAL METHOD

MOLECULAR MECHANICS	SEMI EMPIRICAL	AB INITIO
Very fast speed	Fast speed	Slow speed
Restriction parameters	Good accuracy	Very good accuracy
Very good protein modelling	Good protein modelling	Best protein modelling

XML DOCUMENTATIONS

<computational method>

  <title category="MOLECULAR MECHANICS">

    <speed>Very fast speed</speed>

    <accuracy>Restriction parameters</accuracy>

    <protein modelling>Very good protein modelling</protein modelling>

  </title>

  <title category="SEMI EMPIRICAL">

    <speed>Fast speed</speed>

    <accuracy>Good accuracy</accuracy>

    <protein modelling>Good protein modelling</protein modelling>

  </title>

  <title category="AB INITIO">

    <speed>Slow speed</speed>

    <accuracy>Very good accuracy</accuracy>

    <protein modelling>Best protein modelling</protein modelling>

  </title>

</computational method> 

 XML TREE 

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PROTEIN DATA BANK....(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. 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.<sup>[1]

 HISTORY...</sup>
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. 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.

 

Crystal structure of a LexA protein from Thermotoga maritima

The PDB database is updated weekly (on Tuesday). Likewise, the PDB Holdings List is also updated weekly. As of 21 September 2010 (2010 -09-21)^[update], the breakdown of current holdings was as follows:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	55480	1231	2605	17	59333
NMR	7512	925	162	7	8606
Electron microscopy	214	17	77	0	308
Hybrid	24	1	1	1	27
Other	126	4	4	13	147
Total:	63356	2178	2849	38	68421

For more information , click here

SMILES..(^_^)

SMILES stand for Simplified Molecular Input Line Entry Specification...

• The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

• The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. The terms Canonical and Isomeric can lead to some confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive.
• Typically, a number of equally valid SMILES can be written for a molecule. For example, CCO, OCC and C(O)C all specify the structure of ethanol. Algorithms have been developed to ensure the same SMILES is generated for a molecule regardless of the order of atoms in the structure. This SMILES is unique for each structure, although dependent on the canonicalisation algorithm used to generate it, and is termed the Canonical SMILES. These algorithms first convert the SMILES to an internal representation of the molecular structure and do not simply manipulate strings as is sometimes thought. Various algorithms for generating Canonical SMILES have been developed, including those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT and Chemical Computing Group. A common application of Canonical SMILES is indexing and ensuring uniqueness of molecules in a database.
• SMILES notation allows the specification of configuration at tetrahedral centers, and double bond geometry. These are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed Isomeric SMILES. A notable feature of these rules is that they allow rigorous partial specification of chirality. The term Isomeric SMILES is also applied to SMILES in which isotopes are specified.

Visualization of 3-cyanoanisole as COc(c1)cccc1C#N.

Illustration with a molecule with more of 9 rings, the Cephalostatin-1^[2] (a steroidic trisdecacyclic  pyrazine with the empirical formula C₅₄H₇₄N₂O₁₀ isolated from the Indian Ocean hemichordate Cephalodiscus gilchristi):

Will give, starting by the most left methyle radical on the figure:
C[C@@](C)(O1)C[C@@H](O)[C@@]1(O2)[C@@H](C)[C@@H]3CC=C4[C@]3(C2)C(=O)C[C@H]5[C@H]4CC[C@@H](C6)[C@]5(C)Cc(n7)c6nc(C[C@@]89(C))c7C[C@@H]8CC[C@@H]%10[C@@H]9C[C@@H](O)[C@@]%11(C)C%10=C[C@H](O%12)[C@]%11(O)[C@H](C)[C@]%12(O%13)[C@H](O)C[C@@]%13(C)CO
(Notice the '%' in front of the index of the ring closure labels upper to 9, see the section "Bonds", higher).

Application on some molecules

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate (MIC)	CH3–N=C=O	CN=C=O
Copper(II) sulfate	Cu2+ SO42-	[Cu+2].[O-]S(=O)(=O)[O-]
Œnanthotoxin (C17H22O2)		CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
Aflatoxin B1 (C17H12O6)		O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5
Bergenin (cuscutin) (a resin) (C14H16O9)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2

To get to know more about SMILES click here

chemSketch....... (makes drawing easier) :)

ChemSketch is a PC package which can also be used to draw molecules, reactions, and schematic diagrams and includes powerful optimization and 3D visualization tools. Currently ChemSketch version 11 is available to CDS users. New features and capabilities introduced in version 11 include:

• Interface changes, and new shortcuts and toolbar menus to streamline the workflow
• Improvements in graphical representation, including a NEW 'antialiasing' option for chemical structures
• Combined styles for American Chemical Society (ACS) journals and Royal Society of Chemistry (RSC) journals
• Implementation of an InChI key generator to comply with new IUPAC protocols
• Improved handling of coordination structures
• Augmented handling of images and files, including support of .PNG format 

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.
Benefits:

• Visualize chemical structures in 2D or 3D to gain more insight into spatial configurations, and relationships to molecular properties
• Create professional reports, working with structures, text, and graphics simultaneously
• ACD/ChemSketch also allows you to check other tautomeric forms for your drawn structure. Consideration of tautomeric forms is very important for structure searching, predictions (such as physicochemical properties, i.e., pK_a), and interpretation (i.e., of NMR, MS, and other analytical data). 

See some examples of molecules drawn with ACD/ChemSketch:

	Create Markush structures with variable substitutions
	Special Markush structures with added adn removed mass values or fragments
	Draw complex coordination organometallics
	Show aromaticity and 3D perspective
	Nucleotide and many other biochemical templates are available
	Draw molecular orbital diagrams with ease

 To download ACD ChemSketch, click here

MICROSOFT OFFICE EXCEL

Microsoft Excel (full name Microsoft Office Excel) is a 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 VBA (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 Microsoft Office Excel 2010 for Windows and 2008 for Mac.

Microsoft Excel: Mac 2008 spreadsheet running on

 Graph made using Microsoft Excel

The version of Microsoft Excel...

Excel 2.0
Excel 5.0
Excel 2000
Excel 2007
Excel 2010

For more information click here

MAPLE

MAPLE SOFTWARE

                                                                       Maple Interface 


                                                           

                                                           Plotting of function of two variables

 Example of maple graph

Maple is a general-purpose commercial computer algebra system. It was first developed in 1980 by the Symbolic Computation Group at the University of Waterloo in Waterloo, Ontario, Canada.

Maple allows you to directly manipulate and calculate problems using Mac OS Xs contextual-menu features. When you click on an equation (or part of an equation), a set of context-sensitive commands appear in the menu, letting you perform the most common operations without needing to type in programming syntax. This makes for a slightly less traumatic experience for students and other novice users intimidated by the blinking input cursor.


Maplesoft has been a trusted name in mathematics for over 20 years. By combining the world’s most advanced symbolic computation engine with powerful numeric algorithms, advanced visualization tools, and intuitive interfaces, Maplesoft products enrich your classroom and accelerate your research.

          Products:

	Maple Maple is an essential tool for researchers, teachers, and students in any mathematical discipline. It lets you explore, visualize, and solve even the most complex mathematical problems, reducing errors and providing greater insight into the math.
	Maple. T.A. Maple T.A. is a web-based system for creating tests, assignments, and exercises, automatically assessing student responses and performance. It supports complex, free-form entry of mathematical equations and intelligent evaluation of responses.
	Maple T.A. MAA Placement Test Suite The Maple T.A. MAA Placement Test Suite allows your institution to use the renowned Mathematical Association of America (MAA) placement tests through the online testing environment of Maple T.A.
	E-Books and Study Guides Maplesoft offers study guide and e-book products designed to enhance the teaching and learning of mathematics.
	MapleNet Students can run Maple-created learning materials through a web browser from anywhere in the world--on or off campus--with no other software needed on their machines.
	A Complete Line of Add-On Products A Maplesoft offers an extensive line of add-on products by Maplesoft and third parties, including the Global Optimization Toolbox for Maple.

For more valuable information,click here