ACD/ChemSketch Freeware

ACD/ChemSketch Freeware is comprehensive chemical drawing package, intended for home and educational use only. Among many other features, this product offers IUPAC chemical naming up to 50 functional atoms, prediction of logP, comprehensive report creation, tautomer recognition, 2D structure cleaning, 3D optimization and viewing, drawing of polymers, organometallics, and Markush structures and as well as access to the chemistry Web search engines PubChem, eMolecules, and ChemSpider.

Download Chemsketch Software

How to used ACD CHEM SKETCH

Here are some of my drawing in Chem Sketch:

Energy of Reaction Diagram

Drawing a p-orbital

Drawing a d-orbital

Drawing a pi-type orbital

Drawing Vacuum Distillation Apparatus

Drawing DNA Strand

Drawing Lipid

SMILE

Simplified Molecular Input Line Entry System

SMILES^TM as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols.

SMILES^TM development was initiated by  using the concept of a graph with nodes as atoms and edges as bonds to represent a molecule. Parentheses are used to indicate branching points and numeric labels designate ring connection points. The basic SMILES^TM grammar also includes as well as isotopic information, configuration about double bonds, and chirality leading to what is known as isomeric SMILES^TM. A SMILES^TM string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILES^TM string symbolizing either a molecule or reaction.

Some simple SMILES^TM examples:

Ethanol	CCO
Acetic acid	CC(=O)O
Cyclohexane	C1CCCCC1
Pyridine	c1cnccc1
Trans-2-butene	C/C=C/C
L-alanine	N[C@@H](C)C(=O)O
Sodium chloride	[Na+].[Cl-]
Displacement reaction	C=CCBr>>C=CCI

Since its inception, SMILES^TM has been modified and expanded by Daylight to include not only new features but two additional chemical languages: SMARTS^®, an expansion of SMILES^TM allowing specification of molecular patterns and properties for substructure searching with varying levels of specificity, and SMIRKS^®, a restricted version of reaction SMARTS^® involving changes in atom-bond patterns that define generic reactions.

Here are some examples of SMILE Notation and its Structure from SMILE:

Slide 1

 

 Slide 2

Slide 3

Slide 4

Protein Data Bank

   The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. Hence, PDB is a key resource in areas of structural biology, such as structural genomics. The data, typically obtained by X-ray crystallography or NMR spectroscopybiologists and biochemists from around the world since 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. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. Here are some examples of proteins and it's 3-D structure:

1.  HtrA

Also known as DegP and probably identical to the Do protease, is a heat shock-induced serine protease that is active in the periplasm of Escherichia coli. Homologues of HtrA have been described in a wide range of bacteria and in eukaryotes. Its chief role is to degrade misfolded proteins in the periplasm. Substrate recognition probably involves the recently described PDZ domains in the C-terminal half of HtrA and, we suspect, has much in common with the substrate recognition system of the tail-specific protease, Prc (which also possesses a PDZ domain). The expression of htrA is regulated by a complex set of signal transduction pathways, which includes an alternative sigma factor, RpoE, an anti-sigma factor, RseA, a two-component regulatory system, CpxRA, and two phosphoprotein phosphatases, PrpA and PrpB. Mutations in the htrA genes of Salmonella, Brucella and Yersinia cause decreased survival in mice and/or macrophages, and htrA mutants can act as vaccines, as cloning hosts and as carriers of heterologous antigens.

2. LonA

The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 Å resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal -helix. The structure of the first subdomain (residues 1-117), which consists mostly of -strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.

3. ClP

Members of the Clp family of molecular chaperones and protease regulatory subunits contain homologous regions with properties expected for substrate-binding domains. Fragments corresponding to these sequences are stably and independently folded for Lon, ClpA, and ClpY. The corresponding regions from ClpB and ClpX are unstable. All five fragments exhibit distinct patterns of binding to three proteins that are protease substrates in vivo: the heat shock transcription factor σ³², the SOS mutagenesis protein UmuD, and Arc repressor bearing the SsrA degradation tag. Recognition of UmuD is mediated through peptide sequences within a 24-residue N-terminal region whereas recognition of both σ³² and SsrA-tagged Arc requires sequences at the C terminus. These results indicate that the Clp proteases use the mechanism of substrate discrimination and suggest that these related ATP-dependent bacterial proteases scrutinize accessible or disordered regions of potential substrates for the presence of specific targeting sequences.

HTML

Example of HTML

   "In 1980, physicist Tim Berners-Lee, who was a contractor at CERN, proposed and prototyped ENQUIRE, a system for CERN researchers to use and share documents. In 1989, Berners-Lee wrote a memo proposing an Internet-based hypertext system.Berners-Lee specified HTML and wrote the browser and server software in the last part of 1990. In that year, Berners-Lee and CERN data systems engineer Robert Cailliau collaborated on a joint request for funding, but the project was not formally adopted by CERN. In his personal notes from 1990 he lists "some of the many areas in which hypertext is used" and puts an encyclopedia first.   HTML, which stands for HyperText Markup Language, is the predominant markup language for web pages. A markup language is a set of markup tags, and HTML uses markup tags to describe web pages.
HTML is written in the form of HTML elements consisting of "tags" surrounded by angle brackets (like <html>) within the web page content. HTML tags normally come in pairs like <b> and </b>. The first tag in a pair is the start tag, the second tag is the end tag (they are also called opening tags and closing tags).
The purpose of a web browser is to read HTML documents and display them as web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the page.
HTML elements form the building blocks of all websites. HTML allows images and objects to be embedded and can be used to create interactive forms. It provides a means to create structured documents by denoting structural semantics for text such as headings, paragraphs, lists, links, quotes and other items. It can embed scripts in languages such as JavaScript which affect the behavior of HTML webpages.
HTML can also be used to include Cascading Style Sheets (CSS) to define the appearance and layout of text and other material. The W3C, maintainer of both HTML and CSS standards, encourages the use of CSS over explicit presentational markup.         
One difference in the latest HTML specifications lies in the distinction between the SGML-based specification and the XML-based specification. The XML-based specification is usually called XHTML to distinguish it clearly from the more traditional definition.

HTML	XHTML
Allows many shortcuts	Does not allows shortcuts
Optional opening and closing tag	Requires all elements to have an opening tag and a closing tag