Professional Documents
Culture Documents
Cheminformatics
Bioinformatics Infrastructure Facility
Salam Pradeep
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What is Chemical Informatics
Chemoinformatics or chemical informatics is the use
of computer and informational techniques, applied to
a range of problems in the field of chemistry.
It is the mixing of those information resources to
transform data into information and information into
knowledge for the intended purpose of making better
decisions faster in the area of drug lead identification
and optimization.
In silico techniques are used in pharmaceutical
companies in the process of drug discovery.
These methods can also be used in chemical &
allied industries in various other forms.
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What is Computational Chemistry
A branch of chemistry that uses computers to
assist in solving chemical problems.
Uses the results of theoretical chemistry,
incorporated into computer programs, to
calculate the structures and properties of
molecules & solids.
Its results normally complement the information
obtained by chemical experiments & in some
cases predict unobserved chemical
phenomena.
Widely used in the design of new drugs and
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Chemical & Ligand Databases
Beilstein
Database (Commercial)
NCBI – PubChem
ChemBank
DrugBank
ChemSpider
LOLI database
RX List
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Chemical Similarity Search
ChemBank (Web based)
ACD (Advanced Chemistry Development)
Free Software
Molsoft (Web based)
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Chem Bank
It is a public, web-based informatics environment
created by the Broad Institute's Chemical Biology
Program & funded in large part by the National Cancer
Institute's Initiative for Chemical Genetics (ICG).
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ACD Chemsketch Structure Search
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Molsoft Chemical Search
Molsoft is a La Jolla, California based company that is a primary source of new
breakthrough technologies in modeling, docking, computational chemistry and
biology.
Online Tools:
1. PDB Viewer
2. 2D to 3D Converter
3. Chemical Search
Drug Likeness
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Drug Bank
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Chemical File Formats
File Ext Format Name
alc Alchemy Format
cdx ChemDraw, Cambridge Soft
cer Accelrys MSI Cerius II
c3d Chem3D, Cambridge Soft
cif Crystallographic Information File, CCDC
mol MDL Molfile
smiles, smi Simplified molecular input line entry
specification
sdf Structure-Data File
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Chem Office
A molecule editor developed by the
cheminformatics company CambridgeSoft.
ChemOffice comprises ChemDraw, Chem3D
and ChemFinder.
Available for Apple Macintosh and Microsoft
Windows.
Designed for Chemist and Biologists
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Chem Draw
Chemical structure to name conversion
Chemical name to structure conversion
Structure cleanup
Anti-aliased graphics
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Powerful Features
Convert Name to Structure
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Calculate Properties
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1H NMR Prediction
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Chem Finder
ChemFinder® is a database management
system for working with chemical information.
It provides a place to store chemical
structures, physical properties, notes, tables of
data, and charts based on that data.
With ChemFinder, we can search through data
efficiently and quickly, and we can organize the
data instantly.
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Compound Library
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PASS (Demo 51 Activities)
PASS Professional (Prediction of Activity
Spectra for Substances) predicts the biological
activity spectra for substances on the basis of
their structural formulae, includes SAR Base
(Structure-Activity Relationships data and
knowledge Base) and provides its creating,
updating and training.
Predicts 51 Biological Activities
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Pharmacological Effects
Antihypertensive: Substance used for hypertonia
treatment. Substance reduces the increased arterial
blood pressure.
Vasodilator: Substance that causes relaxation of blood
vessels.
Diuretic: Substance that promotes the excretion of urine
by direct action on kidney function.
Uric acid excretion stimulant: Substance that increases
the urinary excretion of uric acid, thereby reducing the
concentration of uric acid in the blood.
Angiotensin AT2 receptor antagonist: Substance that
binds to the angiotensin AT2 receptor and prevents its
stimulation.
Saluretic: Substance that promotes excretion of sodium
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urine.
Molecular Mechanisms
Calcium channel antagonist Renin inhibitor Neuropeptide Y antagonist Dopamine D1 agonist
Endothelin receptor antagonist Nitric oxide agonist Adenosine receptor agonist Metalloproteinase inhibitor
Endothelin A receptor antagonis Potassium channel activator Nitric oxide donor Adrenaline antagonist
Beta adrenoreceptor antagonist Calcium antagonist Carbonic anhydrase inhibitor Angiotensin antagonist
Beta 1 adrenoreceptor antagonist Kinesin antagonist Guanylate cyclase stimulant Dopamine agonist
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Side Effects and Toxicity
Carcinogenic: Substance that produces cancer.
Embryotoxic: Substance damaging to the
embryo, which may result in death or in
abnormal development.
Teratogen: Substance that causes the
production of physical defects in the developing
embryo.
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ADME / TOX Box Abraham Solvent
Mcgowan volume
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Chem 3D
Chem3D enables to create color models of
chemical and biochemical compounds.
Once we sketch a model, we can calculate a
variety of molecular properties - electrostatic
potentials, bond energies, and spectrum
prediction.
It combines powerful building, analysis, and
computational tools with intuitive menus and a
powerful scripting interface.
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Force Field Calculations
MM2: Most commonly used for calculating
properties of organic molecular models.
- Correlates the potential energy surface to the
conformations of our model
MMFF94: Used to perform energy
minimization calculations on proteins &
biological structure.
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MM2 & MMFF94
Energy Minimization: The atoms location for
a build model is not accurate compared to the
actual one. Hence EM
Molecular Dynamics: Uses Newtonian
mechanics to simulate motion of atoms,
adding or subtracting kinetic energy as the
model’s temperature increases or decreases.
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GAMESS
The General Atomic and Molecular Electronic
Structure System (GAMESS)
A general ab initio quantum chemistry package
maintained by the Gordon research group at
Iowa State University.
Minimize Energy
Compute Properties
Run Frequency
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