CHEM 767: Chem Info Retrieval

Jonathan Soffer's Log

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December 3, 2009:

Terrible news my cume topic was just changed for this saturday...

Rough draft is posted to the main page, I still need to clean it up and it still needs a lot of work....

Wiki main page issues

Reference 31 will not code correctly, even though I have attempted in text editor to code and using the hyperlink button it will not remain linked. I believe the < is the culprit, but I am not positive.

[You can use this link instead of the DOI if it won't work - but please please please get rid of the formatting - I can't even read the references the font is so small JCB]

December 2, 2009:

I think it was a .docx issue with refworks, all of a sudden Word 2008 (after the last update) has been giving me a lot of issues. I resolved it in a very roundabout way.

Side note, I saw my smiles for uvaricin was accepted into Chemspider.
[Yes - excellent work - you can shave off 500 words from your report JCB]

Im actually over 3000 words, I am in the process of cutting it down now...
[You don't have to make it exactly 2500 :) - anything over 2500 is ok JCB]

November 30, 2009:

Ran into an issue with Refworks, even though I have been using it for a few years now, this is my first time using it with SnowLeopard, and it is apparently not compatible with Write-and-Cite. It places the references but will not create the final reference sheet. I will have to double check that I did not alter the code at all. I removed the program and the pref file and reinstalled, I am still getting the same error. I will review the script as this leads me to believe that there is a syntax error somewhere.

[Peggy should be able to help with Refworks problems JCB]

Errors were encountered while processing your file:
  • The following error occurred attempting to read your document : 'this.oRange.Text.substr(...).match(...).0' is null or not an object

Last night I remade the images the images for the paper, I think I am getting much better at using VMD, I had been running into issues with creating movies in VMD, for some reason it will export and then deletes the file it creates, I have sent an email to the developer of fink to see if I installed the software incorrectly, as I am not used to terminal code.

November 22, 2009:

[Nice! So the model you are depicting below shows the protein completely outside the membrane? JCB]
Yes, I found someone that had worked out the coordinate system on how the protein rests/is oriented on the surface of the membrane.


Well I found an new tutorial that does a better job of explaining how to edit the text files and combine all of the files into a gigantic pdb file... the articles seem to all contradict one another with the point of attachment. I assumed it was a lysine residue but now I am not so sure. I will most likely have to make a guess to denote a coordinate system to attach the cyt c to the membrane. I have begun to combine all of the file types to make the final rendering, attached was my first attempt, I have the lysine residues that I believe are attached to the membrane directed at the membrane, but as mentioned it is still not finished.


October 17th, 2009:

Finished assignments 1 and 2 ( I will need to proofread once more) and concluded my reference search for the time being, I added the seemingly significant references to my main project page. I assume that these may change before this project is completed. I am currently trying to organize all of the information I have just read. I believe I now have a better understanding that cyt c has with the membrane, but I am still having issues constructing the membrane, I found a membrane builder tutorial using CHARMM, another program I am slightly familiar with. The membrane proved quite problematic to build in Hyperchem, I recently heard of HyperProtein (beta), but have yet to try it.

I have also updated and organized my other pages to make this wiki more useful in an exam setting. I created a class notes page that I will be able to find in class material much more quickly and have added an assignments page. I have also added a bar to the top of most of my pages that links each of my pages to allow for easier access as the course progresses.[Great idea! JCB]

I just found on the VMD site a short guide o the visualization of membrane bound protein systems. I have now successfully created a uniform 100 x 100 phospholipid bilayer, this was built into the VMD package, it was very easy to render using the membrane builder. I and learning now how to form a non-uniform layer. [Looking good - do you have a server to host an interactive project? JCB]



October 15th, 2009 (Class 4):

To fix the wiki - use text edit, or the notepad
use Digital Object Identifiers in your wiki
use friendfeed to get useful information

Searching - recognize features of SMILE and InChi:
InChI (cannot use Google to search for these, not capable for understanding)
@ denotes chirality
+ - refers to chiral centers

InChI key has two parts:
The Right has the stereochemistry information (this will pull the one searched for in particular)
The Left has the core information (this will pull all matches)

Wikipedia entries are embeded here - very useful

Associated Data sources:
Easy to purchase items, or might find useful things directed to what you are investigating.

Will need the predicted properties part of chemspider for the next HW.

Use SDBS for obtaining spectra or try sigmadirectly.

Kegg deals with metabolic pathways
MeSH descriptors
EPI for environmental info
SimBioSys LASSO - compares against PDB and scores possible interaction with enzymes

Moving onto the next tool: Beilstein Crossfire
Searches through primary sources to get experimental information

October 14th, 2009

I just randomly came across the PDB Wiki in my search and found the site very interesting. There are some great software and database links for all thing protein related. Here is the link for the PDBwiki to Horse Heart Cytochrome c , this is what I am currently studying, (in particular see the links on the bottom), this would be very useful to the study of a new protein. Side note HH Cyt c's PDB code is 1HRC, for those who read this that might not know and are interested.[absolutely - a key part of using the PDB is to identify the protein code JCB]

I found a great dashboard widget for the mac that runs on jmol called protein glimpse. This application will search by the PDBID.

Just finished minimizing the energy and then created the image for cardiolipin in Hyperchem, one of the components of the liposome that I am synthesizing. ( I just realized that when I brought it into VMD it did not save correctly, i.e. the R groups are way too short, when I tried to replace the file the wiki would not allow me to save the item with the same name for some reason so I put a 2 at the end,[When you upload images or files make sure to use very distinct names so others won't accidentally overwrite JCB] but it appears multiple times in the uploaded file area... rather annoying, but now I see I updated this faster then the wiki was able to handle). Anyway, I have gone through the first 3 hour VMD tutorial and learned how to alter the representations. This image below shows my first trial with the cardiolipin (TOCL) in ball and stick mode within, and the Van der Waals radius is shown in a glass rendering surrounding the inside model. I then added a high gloss finish on the outside and this was the result.


Ok, now I have just finished rendering the next component of the liposome that I will be creating, DOPS. I found that I like the last representation that I have made, so I will continue using the same rendering method.


I started my search again for some more good articles... the one that appears relevant I do not have access to. I attempted to search for this article through EX Borrow, but the search came back with no hit. I have just placed my request for this article through ILLiad (Transaction 167071).

Journal Article: Biochemistry (Moscow): Cardiolipin activates cytochrome c peroxidase activity since it facilitates H2O2 access to heme.

October 8th, 2009 (Lecture Notes):

Drexel"s Library Has:
Over 500 DB
Over 20000 Articles

Interlibrary Loans:
EZ Borrow to access through University ID - Simple search performed across many universities (UPenn, PennState) - I dont believe I have tried this but I will in the future.
ILLiad Interlibrary Loan - getting materials we do not have on site at Drexel (I have already used this as well)
RefWorks - citation organizer, helps you to manage and organize citations (already using this, my boss uses Endnote but we can easily import and export the data files). Can cut and paste bibliographic output into the wiki.

Web of Science- cross discipline database - can manipulate the body of literature you are searching for

October 7th, 2009:
Yes, I think I am going to need clarification on the multimedia requirements then. I was thinking I would make a movie of the interaction with the membrane, and try to put in some of my preliminary data into the model to get it to perform some of the actual kinetics that I have seen in my preliminary experiment, I think I will have to modify the text file through hyperchem and then import that into the VMD modeling package from what I have read in the VMD tutorials. As a report I was going to make it into a more so interactive poster that I could imbed in the wiki, possible using flash or something similar. The text would be limited, more so poster style, I was thinking about a page or two providing the background information and what I will be investigating in the near future.

Wolfram Alpha, Endnote mentioned in C&E News digital brief from Sept 14th (I am a bit behind in reading them), this seems to be following pieces of our lectures, and some other interesting possible useful software and websites.

October 6th, 2009:
Okay! I am excited to work on the multimedia project, as long as that is sufficient, [It won't replace the requirement for a text report but the min number of words can be reduced - depending on exactly how ambitious your project is. We can discuss this in the class as well. JCB] I will embed it into a presentation, with some text. I am listening to a presentation by Dr. Xi about cardiolipin as the binding site to the cytochrome c this afternoon, I should be able to get some insight on good articles in reference to this.

Here is where I found the VMD Tutorials

October 6th, 2009:
The 9 papers turned out to be no good, or I was unable to gain access to them... The ones I was really interested in were not in the Drexel catalogue. [That is not a problem - just submit an interlibrary loan - Peggy will show you how this week JCB]

First attempt in learning VMD, I downloaded the tutorials, to help further. Mike Chelen images of the bilayer are inspiring, but again I am a bit reserved about the time I would have to dedicate to this project.[Sure -only do the multimedia component if you think you can put in the time JCB] I have attached the first image I made of cytochrome c, the heme is colored in a metallic red in the center of the image. [Looks great - if you can incorporate the bilayer it will really be nice JCB] I will use another image I created on our groups website, I think it will be really useful there (website image updated already, see interest #3) and for this project I will be adding the liposome (side-note: I had built and maintained the site since joining the Stenner Biospectroscopy group).

cytochrome c


October 4th, 2009:
SciFinder search for "Cytochrome c" + "Liposome" + "Cardiolipin" retrieved 57 articles, some interesting articles found, of those 57 search refinement produced 9 papers that are relevant to what I would like to discuss. Once i read them I will post the article I will most likely use in my project.

October 3rd, 2009 (Post CUME #1):
Thanks, I will look into the suggestions, I knew of a few of the references mentioned, but I will definitely investigate further into the ones I was unaware of! I will post the outcomes or anything else earned there on my log.

October 1st, 2009 (Research [Supplemental]^2 ):
Successfully narrowed my topic down to a future research project that I will be carrying out on Cytochrome c and Liposome Binding (using Cardiolipin) - Mimicking the changes that occur on the surface of a membrane after conversation with JCB. [See if this might be useful for a multimedia project JCB] [Mike Chelen added images of the bilayer produced by the software JCB]

Considering an interactive presentation, but worries about the research and time limitation that I am under, either way I will start by finding articles. Dr. Stenner recommended I read articles by the Kagan Group, I found one and added it to the main page.

October 1st, 2009 (Research Supplemental): Narrowing of the Research Topic
  • Protein Folding and unfolding
  • Cytochrome c - 5 conformational sub-states (note there is new intermediate III*)
  • Cytochrome c and Liposome Binding - Mimicking the changes that occur on the surface of a membrane
  • Circular Dichroism Spectroscopy for the use of Biomolecules

Assignment: Join SciFinder and Successfully log in and perform a search.

October 1st, 2009:
In class: Wiki Review
  • Use of the Text Editor - This will help you fix the text and make use of the format commands
  • Use of Wikitext - See help menu

New Wiki Page: Publishing in Chemistry
Document Source Types:

  1. Primary Source: The Source of the information, nothing that you can cite that provides more info than that source [Journal Article; Conference Proceedings; Patents; Lab Notebook; Blog; ]
  2. Secondary Source:[Review Article; Handbooks; Wikipiedia; Databases; Blog; ]
  3. Tertiary Source: [Magazines; ]

Copyrights: Print Rights arrangement of words is important

Project: Pick a very small area and exhaust it to virtual certainty.

Open Access Journals:
Hindawi Publishing Corp. - Bioinorganic Chemistry and Applications - I have actually participated in an open access journal last year with another group.[That's awesome! JCB] The link is to that article. doi:10.1155/2008/257038 [BTW if you want to convert a doi to a link use JCB]

September 30th, 2009:
I emailed IRT a week or two after the Snow Leopard OS and new iPhone update was released and they said that they were testing this feature currently but were unable to tell me when they could provide me with the Shared Secret code or certificate for the VPN network.

Oh, one other question, am I allowed to se this paper for the basis of the research seminar ? This will help me to decide on the specifics of what my paper will be for this class (this website I created and manage as well).[I don't see a problem with that - but you can't just use text that you or anyone has already written - also note that the text that you post here is under a CC-share alike License which has consequences for reuse - we will discuss that tomorrow in class JCB]

Performed a Scifinder search using the terms "Cytochrome c" + "Liposomes" found 3 really good articles, that were added into the program papers , if you have a mac I highly highly suggest this program it is a pdf organizational lifesaver.[Yes several of my friends with Macs speak highly of it - see some discussions hereJCB]

September 30th, 2009 (this was more so Sept. 29th) :
Just updated the blog list to reflect my suggestions. The ChemMobi iPhone app seems to work well, you can choose discoverygate when on the Drexel campus or Chemspider while off campus. It will be nice once IRT adds the security code so we can log in through our phones and apple computers.[Do you know when IRT plans to do this? JCB] VPN was integrated into the OS in snowleopard.

September 27th, 2009:
I just remembered ScienceBlogs and Seed Magazine are good starting points. I do not believe seed is peer reviewed but they tend to publish some interesting science. [If you want to add these to the blog list that would be ok for now - ultimately we would want to focus on cheminfo and chem blogs - we will discuss peer review in an upcoming class and it would be helpful to look at these websites in that context JCB]

Lipidomics Database

September 26th, 2009:
While avoiding studying for my first cumulative exam, I updated resources page with previously suggested sites, see comments below. I have a variety of other database selections that might be useful to undergrads who are more interested in biochemistry (proteomics, bioinformatics, biophysics etc..), but since they are more biological in nature and I am not sure if it would be useful to the rest of the class. I also have an institutional code to mynetresearch for premium access if anyone is interested.

SwisProt - For the analysis of protein sequences and structures
UniProt - For comparative protein sequence and functional information

[Some bioinformatics tools can be helpful - most especially if you use them in your project. JCB]

September 24th, 2009:
Intro to class/syllabus:
  • Set up Wiki (Completed)
  • Second Life
  • ChemSpider (Downloaded iPhone App a while ago - ChemMobi )[Didn't know about this - please add JCB]
  • Wikipedia
  • Sigma Aldrich
  • Web of Science - Looked at Journal citation list JACS is 13th Most cited in all chemistry journals
  • Added CRC Handbook to the resource Page

Possible addition to Social networks: [Perfect - please add JCB]

Potential Paper Topics:
  • Native and nonnative Conformational Changes of Cytochrome c
PDB - Molecule of the Month 12.2002
  • Unfolding the mystery of protein folding
  • The significance of nonnative conformations of proteins
  • Use of Circular Dichroism for the study of biomolecules
  • Visual Molecular Dynamics the perfect tool for the study of biomolecules and smaller molecules
VMD - Visual Molecular Dynamics[This would be a great platform the multimedia component JCB]**