Last Modified

   1 January 2020

Theoretical Organic Chemistry Nuclear Receptor Chemistry Structural Bioinformatics Rational Drug Design

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Homology Modeling Professional for HyperChem

Click on the individual program names to access to their detailed features.


Ramachandran Plot



The "Ramachandran Plot" program is mainly used for the final assessment of the models. Alternatively, this program can simultaneously change the main-chain conformation using circle on the Ramachandran Plot window, which represent the corresponding f and y angles of the 3D structure in the HyperChem workspace. The altered conformation can be easily reverted to the original and vice versa. Moreover, the new f and y angles can be prepared as a restraint condition for the subsequent structural optimizations and molecular dynamics calculations. For example, this function can be used for logically giving an antagonist form from the corresponding agonist form.



* Three f and y regions (light-red, light-blue, and yellow regions) have been statistically determined based on about 4,000 X-ray crystal structures (without overlap of the same proteins in about 25,000 structures) in the range of 0.0-4.0 resolutions.




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