Weekly JournalHere are weekly journal entries documenting my DREU experience.
|
Week 1 - Getting Settled
After being abruptly introduced to Houston's heat and humidity, I got a tour of the lab and the room I would be working in. I was also introduced to the other undergraduate who is working on the same project, Angela Hoch, as well as another undergraduate in the lab for the summer and several grad students in the lab group.
I got set up with Rice (got ID card, key, web account).
I started reading up on the project and background information on protein docking to get a better understanding of the problem we are addressing.
I got set up with Rice (got ID card, key, web account).
I started reading up on the project and background information on protein docking to get a better understanding of the problem we are addressing.
Week 2 - Installation
I met Didier Devaurs, a post-doc who has been working on DINC for a while, and I started playing around with the DINC web server to assess the interface and familiarize myself with the program. Then, I downloaded and installed DINC to my PC, which took the better part of a day because of various installation issues, and the fact that I didn't have administrative rights on my machine.
After successfully installing DINC, I ran it with the same sample input I ran on the web server, to make sure it was installed correctly and to see how the program output worked. Also, I tested that I could run the DINC server locally on my machine.
Now I'm all set to begin looking at the feedback Angela and I had on the web server and start to code!
After successfully installing DINC, I ran it with the same sample input I ran on the web server, to make sure it was installed correctly and to see how the program output worked. Also, I tested that I could run the DINC server locally on my machine.
Now I'm all set to begin looking at the feedback Angela and I had on the web server and start to code!
Week 3
This week I worked on implementing:
- Timer to show how long a job has been running on the web server
- Updating DINC to work with latest version of Autodock
I also started trying to implement the ability to input grid dimensions in angstroms instead of grid points.
I also ran more jobs with just Autodock to better understand the program, and to test what Autodock/Autogrid does when a receptor has ions. It does not like it.
I ran into problems running DINC locally on my machine, so I have to either ssh into a different machine in the lab, o or if I'm running the web server I use my laptop.
- Timer to show how long a job has been running on the web server
- Updating DINC to work with latest version of Autodock
I also started trying to implement the ability to input grid dimensions in angstroms instead of grid points.
I also ran more jobs with just Autodock to better understand the program, and to test what Autodock/Autogrid does when a receptor has ions. It does not like it.
I ran into problems running DINC locally on my machine, so I have to either ssh into a different machine in the lab, o or if I'm running the web server I use my laptop.
Week 4
This week I
- Finished implementing the timer
- Ran Autodock/Autogrid with a receptor with a couple ions to see how Autodock deals with it. It doesn't, unless you provide parameters for the ions, which would be difficult to incorporate into DINC.
- Implemented small tweaks to the results page
- Found that you can move translationally in JSmol if you hold shift and double click before moving the mouse
We also discussed the larger project I'll be focused on for the rest of the summer, which is to investigate consensus scoring and how we can use that with DINC.
- Finished implementing the timer
- Ran Autodock/Autogrid with a receptor with a couple ions to see how Autodock deals with it. It doesn't, unless you provide parameters for the ions, which would be difficult to incorporate into DINC.
- Implemented small tweaks to the results page
- Found that you can move translationally in JSmol if you hold shift and double click before moving the mouse
We also discussed the larger project I'll be focused on for the rest of the summer, which is to investigate consensus scoring and how we can use that with DINC.
Week 5
I fixed some bugs in DINC regarding the atom names of the final results and fixed JSmol’s issue with changing the ligand visualization when the ligand is protein.
Regarding consensus scoring:
I played with Autodock Vina, discovering that the scoring function can be separated from the sampling function and applied to an already docked ligand + its protein. I will probably be implementing DINC using Vina instead of AutoDock4, and then we will combine the two implementations to use consensus docking.
Regarding consensus scoring:
I played with Autodock Vina, discovering that the scoring function can be separated from the sampling function and applied to an already docked ligand + its protein. I will probably be implementing DINC using Vina instead of AutoDock4, and then we will combine the two implementations to use consensus docking.
Week 6
I worked on incorporating Vina into DINC. I encountered a problem with file formats, as it Vina input ligand must be in a different format than DINC currently creates.
This week was also the 4th of July, so I had a nice long weekend.
This week was also the 4th of July, so I had a nice long weekend.
Week 7
I implemented the ability to rescore all the intermediate and final confirmations in DINC with Vina, then researched the different ways to implement consensus scoring.
Week 8
After discussing with Didier, we decided that only using Autodock and Vina for scoring wasn't enough for real consensus scoring, but it would be good to compare DINC using Autodock to DINC using both. We also decided that we should also compare it to DINC using Vina, so I spent the week implementing that version of DINC.
Vina has less diverse output than Autodock, so the results we get from DINC using Vina are more similar to each other than the results from DINC using Autodock. The clustering part of DINC does not work using Vina because almost every output conformation is in the same cluster.
Vina has less diverse output than Autodock, so the results we get from DINC using Vina are more similar to each other than the results from DINC using Autodock. The clustering part of DINC does not work using Vina because almost every output conformation is in the same cluster.
Week 9
This week I finish the version of DINC that uses Vina. To diversify the results more I had to increase the range in energy between the lowest and highest scoring conformations. Vina is more of a black box than AutoDock, and you have less control over the number of output conformations, but I was able to increase them a little. The DINC-vina results are still not as diverse as AutoDock, but maybe that's a good thing because the Vina results are more accurate.
I tested each of the three versions of DINC with redocking experiments uses a ligand whose PDB label is 4d0d. The results show that DINC-Vina and DINC-hybrid (the consensus scoring version of DINC) are more accurate than original DINC.
I compiled my work for the summer in a powerpoint to present to the group on Monday, which will be turned into a poster next week for the IBB poster session next Friday.
I also had a family reunion on the weekend so I was out of town Friday-Sunday.
I tested each of the three versions of DINC with redocking experiments uses a ligand whose PDB label is 4d0d. The results show that DINC-Vina and DINC-hybrid (the consensus scoring version of DINC) are more accurate than original DINC.
I compiled my work for the summer in a powerpoint to present to the group on Monday, which will be turned into a poster next week for the IBB poster session next Friday.
I also had a family reunion on the weekend so I was out of town Friday-Sunday.
Week 10
The final week! This week was mainly spent on writing my report and creating my poster. I also made some small changes to the DINC code that will make it easier for the other members of the lab to continue my work when I'm gone. They are planning on benchmarking the three versions of DINC, and keeping me in the loop. Maybe I'll have time this coming semester to help them with that remotely, but I'll have to see.