introduction

The three-dimensional structure of a molecule is closely related to

a large variety of chemical, physical and biological properties.

The need for 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.

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

GENERATE ACCURATE 3D COORDINATES:CONCORDHistory: (Texas, 1987)

Concord is productivity tool useful for molecular modeling and QSAR/QSPR research

Concord is the oldest program generates 3Dstructures which are 100% consistent with the stereo-chemical specifications in the 2D input.

Advantages :

Fast, Accurate Structures : extremely rapid

Fast, Complete Conversions :• providing complete control regarding the quality of

structuresin 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 .

Concord provides many advantageous input/output options

MDL SD-files, SYBYL® mol and mol2 files, and Tripos’ SLNformats are supported.

The highly compact and easy-to-learn SMILES line-notation isanother very popular input format. Additional output formatsinclude

MOPAC, MM4, GAUSSIAN,PDB, CSSR, ORTEP, and customformats. To save time, two or more formats can be outputsimultaneously.

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).

GASPTM

StereoPlex®

GeneFold®

FlexXTM

:StereoPlex

,

when coupled with Concord, enables the intelligent stereochemical diversification of a database.

•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

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 (0.14s/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 computationtimes refer to the number of structures converted by the different programs

:These quantity-qualitycharacteristics show again the different suitability of the seven programs for automatic2D-to-3D conversion.

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 accurateEasily and conveniently stored, edited, and duplicated ,