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Structure Guided Drug Discovery

SGDD: Recipes, Ideas and Links...

Jagadeesh Mavinahalli has sent you a hi5 Friend Request

Sunday, May 18, 2008
hi5 Update

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I set up a hi5 profile and I want to add you as a friend so we can share pictures and start building our network. First you need to join hi5! Once you join, you will have a chance to create a profile, share pictures, and find friends.


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Structure search by name (IUPAC Nomenclature search)

Thursday, September 15, 2005

Search IUPAC Nomenclature

You know the name of a compound, say methylenedioxy, but do not know the structure of it. One of the easiest online way is to search for compound name in http://www.acdlabs.com/iupac/nomenclature/#search

Search for methylenedioxy resulted in following output:

A cyclic acetal in which the two acetal-oxygen atoms form part of a ring may be named: (a) as a heterocyclic compound; (b) by use of the prefix "methylenedioxy-" for the group as a substituent in the remainder of the molecule, derivatives of the methylenedioxy group being named as substitution products thereof; or (c) particularly when stereochemistry is implied in the name of the corresponding alcohol or ketone, as the alkylene or alkylidene derivative of that alcohol or as the alkylene or alkylidene acetal of that ketone.

PyMol: A beautiful open-source software for molecular visualization

Tuesday, August 16, 2005
Present version is 0.98. I love this software and have been a happy (power)user of this software since 2003.
PyMol is here to grow.

A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. Supports Windows, Mac OSX, Unix, and Linux.

Image Galleary


Good Tutorial for new users

PyMOL Wiki

PyMOL users Group

Useful PyMOL Scripts

From PyMOL Introduction page:
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.

The extensible core PyMOL module (hosted here at SourceForge) is available free to everyone via the "Python" license (a simple BSD-like permission statement), but we ask all users to purchase a license and maintenance agreement in order to cover our development and support costs.

In order to motivate such sponsorship, we offer support and other incentives to PyMOL licensees with current maintenance subscriptions. In this way, we seek to insure the viability of the Open-Source project by providing a specific incentive (or reward) for outside support. However, our hope is that only a small subset of PyMOL's total value will need to be restricted to Incentive packages -- just enough to justify regular contributions and keep the project self-sustaining.


Friday, August 12, 2005
Structure-Guided Drug Design
Structure-Guided Drug Discovery