Genome Assembly – Olympia Oyster Illumina & PacBio Using PB Jelly w/Platanus Assembly

Sean had previously attempted to run PB Jelly, but ran into some issues running on Hyak, so I decided to try this on Emu.

Here’s a brief rundown of how this was run:

See the Jupyter Notebook for full details of run (see Results section below).

Results:

Output folder: http://owl.fish.washington.edu/Athaliana/20171113_oly_pbjelly/

This completed very quickly (like, just a couple of hours). I also didn’t experience the woes of multimillion temp file production that killed Sean’s attempt at running this on Mox (Hyak).

However, it doesn’t seem to have produced an assembly!

Looking through the output, it seems as though it didn’t produce an assembly because there weren’t any gaps to fill in the reference. This makes sense (in regards to the lack of gaps in the reference Illumina assembly) because I used the Platanus contig FASTA file (i.e. not a scaffolds file). I didn’t realize PB Jelly was just designed for gap filling. Guess I’ll give this another go using the BGI scaffold FASTA file and see what we get.

Jupyter Notebook (GitHub): 20171113_emu_pbjelly_22mer_plat.ipynb

PKA as target

My docking experiments of OSM-S-106 vs all crystal structures of Plasmodium kinases supports PKA (protein kinase A) as the top target (PDB 5kbf).

OSM-S-106 was docked into the ligand binding site with the target side chains free to rotate as described in the previous entry. The docked structure was then energy minimized in Yasara with the Yasara2 force field with explicit water molecules in a 6A dodecahedral box. Three cycles of simulated annealing energy minimization were performed. The energy minimized coordinates are attached. Visual inspection showed that OSM-S-106 was bound quite tightly in its pocket, especially the sulfonamide end, leaving little room for chemical extension. This would be consistent with the SAR data.

All the compounds in Series 3 were then aligned to the cAMP site using a combined ligand-based and force-field based method in Cresset Forge, with protein structure (pdb 5kbf) set as medium strength restraints. I then created a number of modifications of OSM-S-106 that I considered compatible with the binding mode. OSM-S-106 had a Cresset Forge Sim score of 0.606. The following compounds had similar or better Sim scores.

OSM-S-106-5   Sim=0.637
OSM-S-106-3   Sim=0.608
OSM-S-106-4   Sim=0.600
OSM-S-106-6   Sim=0.570

I do not place much weight in these scores. Rather, I interpret them as meaning that these compounds are worth exploring experimentally. Compounds are attached as MarvinSketch (Chemaxon) files.


PKA as target

My docking experiments of OSM-S-106 vs all crystal structures of Plasmodium kinases supports PKA (protein kinase A) as the top target (PDB 5kbf).

OSM-S-106 was docked into the ligand binding site with the target side chains free to rotate as described in the previous entry. The docked structure was then energy minimized in Yasara with the Yasara2 force field with explicit water molecules in a 6A dodecahedral box. Three cycles of simulated annealing energy minimization were performed. The energy minimized coordinates are attached. Visual inspection showed that OSM-S-106 was bound quite tightly in its pocket, especially the sulfonamide end, leaving little room for chemical extension. This would be consistent with the SAR data.

All the compounds in Series 3 were then aligned to the cAMP site using a combined ligand-based and force-field based method in Cresset Forge, with protein structure (pdb 5kbf) set as medium strength restraints. I then created a number of modifications of OSM-S-106 that I considered compatible with the binding mode. OSM-S-106 had a Cresset Forge Sim score of 0.606. The following compounds had similar or better Sim scores.

OSM-S-106-5   Sim=0.637
OSM-S-106-3   Sim=0.608
OSM-S-106-4   Sim=0.600
OSM-S-106-6   Sim=0.570

I do not place much weight in these scores. Rather, I interpret them as meaning that these compounds are worth exploring experimentally. Compounds are attached as MarvinSketch (Chemaxon) files.


Predicting targets for Series 3 active compounds

I focused on OSM-S-106, the most active of the Series 3 compounds. I docked OSM-S-106 vs all Plasmodium falciparum kinase crystal structures in the PDB, using smina, the Vinardo scoring function, and flexible side chains.

PDB Name Score
4qox CDPK4 -10.3
4mvf CDPK2 -8.7
3ltt CLK1 -11.8
5kbf PKA-R -13.0
2yog thymidylate kinase -11.4
2bsx purine nucleoside phosphorylase -9.4
1v0p PfPK5 -11.4
5lm3 nicotinic acid mononucleotide adenylyltransferase cannot dock
5tpx Bromodomain Gcn5 -9.7
5llt NMNAT1 cannot dock
3q5i CDPK1 -10.0

More negative scores are better. Top scores go to 5kbf (PKA-R), 3ltt (CLK1), 2yog (thymidylate kinase), 1v0p (PfPK5), with 5kbf considerably better than the others.

Docked complexes are attached below as zipped pdb files.

Predicting targets for Series 3 active compounds

I focused on OSM-S-106, the most active of the Series 3 compounds. I docked OSM-S-106 vs all Plasmodium falciparum kinase crystal structures in the PDB, using smina, the Vinardo scoring function, and flexible side chains.

PDB Name Score
4qox CDPK4 -10.3
4mvf CDPK2 -8.7
3ltt CLK1 -11.8
5kbf PKA-R -13.0
2yog thymidylate kinase -11.4
2bsx purine nucleoside phosphorylase -9.4
1v0p PfPK5 -11.4
5lm3 nicotinic acid mononucleotide adenylyltransferase cannot dock
5tpx Bromodomain Gcn5 -9.7
5llt NMNAT1 cannot dock
3q5i CDPK1 -10.0

More negative scores are better. Top scores go to 5kbf (PKA-R), 3ltt (CLK1), 2yog (thymidylate kinase), 1v0p (PfPK5), with 5kbf considerably better than the others.

Docked complexes are attached below as zipped pdb files.

The Synthesis of anti-malarial investigation

Malaria is a majority of dangerous disease in some poor area,  which will kill a lot of people. Also, there are most of drug which has drug resistance. Hence, Open Source Malaria was created in that moment. This experiment is included in the project of Open Source Malaria. This experiment uses 2,6-dichloropyrazine as the start material. During the whole produces, the experiment used the Thin layer chromatography(TLC), which uses molecular polar to separate mixture and check the reaction to be reacted and Nuclear Magnetic Resonance spectroscopy (NMR), which can identify the different chemical environmental hydro to make sure about the purify product. Both of them are useful technologies, to analysis and check whether the each step’s product is purification. Otherwise, there is some errors in experiment. Finally, the experiment could not do the last step to synthesis the target because some compound or some chemical environment which can not allow the reaction to be done. The experiment is unsuccessful.  

 

REPORT

report.docx

 

POSTER

poster yang.pptx