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.

PASSprovides

simultaneous predictions of many

types of biological activity based on the structure
of organic compounds.

Thus,PASScan

be used to estimate the biological

activity profiles for virtual molecules, prior to their
chemical synthesis and biological testing.

General Information
PASS

...

does computational predictions of biological activity

spectra for drug-like compounds.

uses 2D chemical structures from SD or MOL files.

predicts activities qualitatively.

gives probability estimates for every prediction.

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.

in 2007, 3,300 biological activities.

in 2009, 3,750 biological activities.

in 2011, 4,366 biological activities.

in 2012, 6,400 biological activities.

What can PASS do?

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

The output contains the following predicted activities:

Generaloverview of all biological activities assigned to the input

compound (out of a list of 7527 items)

Pharmacotherapeuticeffects(464; example:antimetastaticeffect)

Biochemicalmechanisms(3850; example:xanthine oxidase inhibitor)

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

Metabolism(195; example:CYP2D6 substrate)

Generegulation 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

TheBiological Activity Spectrumof 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

Some practical examples

Some practical examples