pass and chem bio

PASS PREDICTION OF ACTIVITY SPECTRA FOR

SUBSTANCES

What is PASS !!!

A software product designed as a tool for evaluating the general biological potential of an organic drug-like molecule.

PASS provides simultaneous predictions of many types of biological activity based on the structure of organic compounds.

Thus, PASS can be used to estimate the biological activity profiles for virtual molecules, prior to their chemical synthesis and biological testing.

General Information

PASS ...o does computational predictions of biological activity

spectra for drug-like compounds. o uses 2D chemical structures from SD or MOL files. o predicts activities qualitatively. o gives probability estimates for every prediction. o has an average prediction accuracy of 95%.

Brief history of PASS.

In 1996, PASS could predict only 114 biological activities .

in 1998, 541 biological activities.

in 2005, 2,500 biological activities.





What can PASS do?

The input compound can be submitted in MOLfile or SDfile format.

The output contains the following predicted activities:

• General overview of all biological activities assigned to the input compound (out of a list of 7527 items)

• Pharmacotherapeutic effects (464; example: antimetastatic effect)

• Biochemical mechanisms (3850; example: xanthine oxidase inhibitor)

• Toxicity, i.e. adverse and toxic effects (321; example:arrhythmogenic)

• Metabolism (195; example: CYP2D6 substrate)

• Gene regulation expression (1610; example: VEGF expression inhibition)

• Transporter-related activities (68; example: sodium/calcium exchanger inhibitor)

PASS can quickly predict biological activity spectra for organic drug-like compounds qualitatively. The activities that can be predicted range from pharmacotherapeutic effects, biochemical mechanisms and toxic and adverse effects to influence on the metabolism, gene regulation and transporter-related activities. The software runs under Windows.

PASS has been developed by Vladimir Poroikov, Dmitry Filimonov & Associates currently working in the Department for Bioinformatics at the Institute of Biomedical Chemistry, Russian Academy of Medical Sciences in Moscow.

Biological Activity Spectrum

The Biological Activity Spectrum of a chemical compound is the set of different types of biological activity that reflect the results of the compound's interaction with various biological entities.

Biological activity is defined qualitatively ("yes"/"none") suggesting that the biological activity spectrum represents the "intrinsic" property of a substance depending only on its structure and physical-chemical characteristics.

Though this may be a generalization, it provides the possibility for combining information from many different sources in the same training set, which is necessary because no one particular publication comprehensively covers all the various facets of the biological action of a compound.

ChemBioFinder

ChemBioFinder for Office

ChemBioFinder for Office is installed when you install ChemBioOffice Ultra. This application lets you search for chemical structures in data sources such as documents and databases.

You can browse these types of sources:

Microsoft Word documents

Microsoft Excel spreadsheets

ChemBioFinder databases

Chem & Bio Draw files

ChemBioFinder

You can search files by:

chemical structure

chemical formula

molecular weight

You can also run structure searches using the Chem & Bio Draw plug-in:

substructure

full structure

similarity

identity

Searching by chemical structure

You can find chemicals based on their structure .

You can apply either a substructure, full structure, similarity or identity search.

Note: Any search method that you use in ChemBioFinder you can also use in ChemBioFinder for Office .

Searching by multiple properties

You can search for a chemical structure, chemical formula, molecular weight, or any combination of these properties simultaneously.

To search for other properties or more than one property at a time:

1. Click New Search.

2. Take the appropriate action:

ChemDraw

ChemDraw

ChemDraw is the drawing tool of choice for chemists to create publication-ready, scientifically intelligent drawings for use in ELNs, databases and publications and for querying chemical databases.

A chemical drawing solution that chemists across multiple chemistry disciplines can trust to accurately handle and represent organic, organometallic and polymeric and biopolymer materials (including amino acids, peptides and DNA and RNA sequences) and to deal with advanced forms of stereochemistry.

ChemDraw

Chemists who use ChemDraw to predict properties are able to save time and reduce costs by identifying compounds that are likely to have the desired properties before actually synthesizing them.

Chemists can also save time and increase data accuracy using ChemDraw to generate spectra, construct correct IUPAC names, and calculate reaction stoichiometry.

A powerful set of tools to handle substructural query types (such as variable points of attachment, Rgroups, ring/chain size, atom/bond/ring types, and generic atoms) ensures that compounds are quickly and accurately located by searches, no matter how they are stored in commercial, public or in-house databases.

Calculate The Stoichiometry

Draw a table containing the names and the chemicals compounds

Drawing Way DNA

Get the chemical properties of the compound

Showing chemical compound in Hologram

Integration and assembly of more than amide way

ChemBio3D

ChemBio3D

a powerful desktop modeling program that enables chemists and biologists to generate 3D models of small molecules and biochemical compounds and to perform a variety of calculations and actions on the models to explore properties and interactions.

Benefits(Advantages)

visualization and calculations enable scientists to make better, faster decisions on where to focus their research in order to achieve their research goals sooner.

Students can use ChemBio3D to achieve a better understanding of the 3D nature of molecules (structures, shape in vacuum,properties,....etc)

Runs on modest desktop systems and does not require high performance computing and high end graphics.

ChemBio3D is integrated with ChemBioDraw, making interchange of structures between 2D and 3D modes simple and communication between synthetic chemists and computational chemists productive and open.

Benefits(Advantages)

ChemBio3D includes optional versions of (the semi-empirical modeling program MOPAC, semi-empirical and ab initio molecular orbital).

Integration with these applications provides researchers with additional functionality over property and other modeling calculations using the ChemBio3D.

ChemBio3D enables chemists and biologists to explore the three dimensional shapes and properties of small molecules and biochemicals .

ChemBio3D also allows scientists to save and open standard computational file formats/multiple file formats (such as Gaussian and MOPAC formats) facilitating better communications with molecular modelers and computational chemists.

Some practical examples