Gold Refresher/DNA Sequencing

Fitness  S(hb_ext) S(vdw_ext)  S(hb_int)    S(int)  time          File name              Ligand name

Top 3 Ligands Ligand #3 – 8 84.63       7.25      59.46       0.00      -4.38   81.609    ‘./gold_soln_DHFRvsCB-Kin-UT_m8_1.sdf’  ‘7904503|CB-kin_UT|sdf|2705|dock9’

Ligand #2 – 9 84.90       0.00      63.94       0.00      -3.02   102.960    ‘./gold_soln_DHFRvsCB-Kin-UT_m9_4.sdf’  ‘5826015|CB-kin_UT|sdf|100|dock7’

Top Posed Ligand – 10 81.67       0.00      64.98       0.00      -7.67   201.574   ‘./gold_soln_DHFRvsCB-Kin-UT_m10_5.sdf’  ‘7844633|CB-kin_UT|sdf|2340|dock2

(Above)- This week was the GOLD refresher and the top 10 ligands are shown in the text above.

The ligands found bound differently in the active site of the DHFR protein and had significatly less polar contacts in their images when comapred to the natural substrates MTX, NDP, and NDP. The natural substrates held tightly because they do not have to rotate or worry about steric clashing interfering with bonding. I will say that when running a huge ligand file, it might be good to run it on multiple processor, so the GOLD job choose which ligands best fit in the active site in a more timely matter. (Sorry This Post is so late, but my ligand files took forever to complete). The ligand file I worked with in the lab was the UT_kin_CB.sdf file, and I think most people used the Chembridge.sdf file, therefore results for the top ligands will vary. Also, a little update on my PCR for my protein target. I have not started yet, as I am still waiting on my DNA sequence results. I got the one back from my pNIC, but I had to redo the one for my target protein over again. I used pNIC in both centrifuge tubes the first time my DNA sequence was submitted. There is not much analysis or anything from this week, so I am just doing LAB 2.14 Weekly News Report