Posing Small Molecules
Hello, I was wondering if there is a way to place in a molecule into a DNA and then minimize that structure either with chimera or in combination with other programs using chimera. For example, on page "1928" of the paper I attached they discuss posing a small molecule in between bases of the DNA. Here's the paragraph and the underlined sentences are of interest to me. If you are wondering why I don't use DeepView for this, my answer is that it is very unstable and crashes more often then producing useful results. Thanks for your help in advance. In a second stage, the crystallographic receptors were replaced by canonical B-DNA with similar sequences, generated with X3DNA.49 Since structural changes in the macromolecule are not allowed during docking, one canoni- cal oligomer was previously modified to include an “inter- calation gap”. In this way, Swiss PDB Viewer was used to pose an ellipticine molecule between two base pairs of canonical DNA, parallel to the base rings. After that, the complex was minimized by the steepest descent method, using the GROMACS package with the GROMOS 53A6 force field. The result was a modified B-DNA in which the base pairs flanking ellipticine were separated by 6.50 Å. Ellipticine was removed from the complex, and the modified B-DNA (see Figure 6B/F) was used as a target for docking with ellipticine. The sequences of the X3DNA generated oligomers are d(CGCAATTGCG)2 (without gap) and d(CG- GCATGCCG)2 (with gap, indicated in bold) .
Yes, you could try moving structures by hand. The structures can be activated/deactivated so you can move one while the other one stays in place when you use the mouse: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html> There is no feature that will automatically put the molecules together for you. For that, you would have to use some other program such as DOCK. <dock.compbio.ucsf.edu/> After the molecules are in place, you can energy-minimize (for example, using menu item Tools... Structure Editing... Minimize Structure). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> However, be aware that minimizing in Chimera is fairly slow. You may want to freeze some atoms in place with the "Fixed atoms" option and set "Conjugate Gradient Steps" to 0, at least at first. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 14, 2011, at 7:35 PM, Yoshus Kumka wrote:
Hello, I was wondering if there is a way to place in a molecule into a DNA and then minimize that structure either with chimera or in combination with other programs using chimera. For example, on page "1928" of the paper I attached they discuss posing a small molecule in between bases of the DNA. Here's the paragraph and the underlined sentences are of interest to me.
If you are wondering why I don't use DeepView for this, my answer is that it is very unstable and crashes more often then producing useful results.
Thanks for your help in advance.
participants (2)
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Elaine Meng -
Yoshus Kumka