Automatic Analysis Of Molecular Flexibility
2
3
Entering edit mode
12.6 years ago
Flow ★ 1.6k

We want to test some enhanced scoring function in docking of flexible ligands. Our main bootleneck is the automatic analysis of ligand flexibility, i.e., which parts or fragments of the molecule to consider rigid and which not, for example, in terms of flexible dihedral angles. We wonder if there are open source libraries (not another programs) which we could use for such purpose.

PS: I got information that there is a possibility to do this with Chemistry Development Kit (Egon Willighagen)

PS2: Another option seems to be OpenBabel since it can detect rotatable bonds

analysis • 3.2k views
ADD COMMENT
4
Entering edit mode
12.6 years ago

Yes, the Chemistry Development Kit can do that. Just as an example, there is a Rotatable Bond Count descriptor implemented.

There are various approaches you can take, and it depends a bit on what you qualify something as a rigid bond. We have functionality to

ADD COMMENT
2
Entering edit mode
12.6 years ago

Flexible ligand docking is for now de facto parameter for docking. So you can use any of the docking software: AutoDock/AutoDock Vina for example.

ADD COMMENT
0
Entering edit mode

I said library not another program

ADD REPLY
0
Entering edit mode

sorry for the confusion, I have updated the question

ADD REPLY
0
Entering edit mode

anyway, could autodock do that?

ADD REPLY
0
Entering edit mode

in term of library - try OpenEye Omega

ADD REPLY
0
Entering edit mode

and yes, autodock can do that

ADD REPLY
0
Entering edit mode

OpenEye Omega can only generate conformers, but I do not see information related to fragment/flexibility analysis

ADD REPLY
0
Entering edit mode

Sorry, I don't understand. There is bond - it can be aromatic thou not flexible. All others are mostly flexible even in the rings. OpenEye Tools can clearly state which bond is flexible and which are not.

ADD REPLY

Login before adding your answer.

Traffic: 1512 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6