computational techniques

2. introduction
The three-dimensional structure of a molecule is closely related to
a large variety of chemical, physical and biological properties.
The needfor computer-generated 3D molecular structures has
clearly been recognized in drug design and many other areas.
Since the number of experimentally determined molecular
geometries is limited—about 600,000 X-ray structures
are presently contained in the Cambridge Structural Database ,
there is a need for methods to predicting 3D coordinates directly
from the constitution of a molecule.

3. intro. cont .
As a consequence, in the last three decades a number of programs
for automatic 2D-to-3D conversion have been reported , Among
them,
CORINA (Coordinates) CONCORD CHEM-X etc…
automatically generates three-dimensional coordinates for the
atoms of a molecule purely from its constitution of a molecule,
The program scope, its reliability, robustness and speed as well as
some special features for handling large rings and metal
complexes make it extremely useful for any study or modeling
purpose that requires 3D information of the molecules under
investigation

4. GENERATE ACCURATE 3D COORDINATES:CONCORD
History: (Texas, 1987)
Concord is productivity tool useful for molecular
modeling and QSAR/QSPR research
Concord is the oldest program generates 3D
structures which are 100% consistent with the stereo-
chemical specifications in the 2D input.

5. Advantages :
Fast, Accurate Structures : extremely rapid
Fast, Complete Conversions :
• providing complete control regarding the quality of
structures
in 3D databases.
• Concord allows researchers to specify limits on molecular
size, number of rotatable bonds, etc. and exclude compounds
from the “conversion domain
• Concord typically converts over 99% of the structures in its
conversion domain at an average rate of just 0.2 cpu_seconds per
compound .

6. Concord provides many advantageous input/output options
MDL SD-files, SYBYL® mol and mol2 files, and Tripos’ SLN
formats are supported.
The highly compact and easy-to-learn SMILES line-notation is
another very popular input format. Additional output formats
include
MOPAC, MM4, GAUSSIAN,PDB, CSSR, ORTEP, and custom
formats. To save time, two or more formats can be output
simultaneously.

8. Concord requires a Concord software
license, and is accessible through the SYBYL
expert molecular modeling environment or
standalone. Concord runs on workstations
operating under IRIX® (SGI®) or Linux®
(x86).

9. GASPTM
StereoPlex®
GeneFold®
FlexXTM
:StereoPlex
,
when coupled with Concord, enables the
intelligent stereochemical diversification of
a database.

10. •CORINA is applicable to the entire range of
organic chemistry
•CORINA generates by default one low-energy
conformation for each input structure. For rings
consisting of less than nine atoms, multiple
conformations can be generated—a useful feature
for flexible 3D database search

12. Conversion Rate. CORINA rate (100%
Correctness of StereochemistryAll programs
except Chem-X (23 failures)retained
the stereochemistry of almost all stereocenters
Computation Time. CONCORD requires extremely
short computation times (0.14
s/mol), whereas MOLGEO, and COBRA need
substantially larger times (3.49-8.98 s/mol). All other
programs need times of less than 1 s/mol. The
computation
times refer to the number of structures converted by the
different programs

13. :These quantity-quality
characteristics show again the different suitability of the
seven programs for automatic
2D-to-3D conversion.

14. X-ray and NMR method is very expensive
and difficult and Could take several work
months to process one proteins
Conclusion:
computational methods are Geometrically
accurate
Easily and conveniently stored, edited, and
duplicated
,