How am I supposed to organize a protein database when I can't even organize my address book?
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This document discusses challenges in organizing protein and human databases using cheminformatics approaches. It provides examples of using algorithms to determine if protein or small molecule structures are the same, but questions how useful this is given the complex nature of proteins and humans. While cheminformatics has been very successful in organizing small molecule data, the document argues it may not directly transfer to domains like proteins or human identities that are more complex and context-dependent. The conclusion is that cheminformatics approaches could potentially be used for indexing related domains, but their power is limited when logical assumptions break down, such as determining the number of individuals with the same name.
How am I supposed to organize a protein database when I can't even organize my address book?
- 1. How am I supposed to organize a protein database when I can't even organize my address book? Jeremy Yang UNM & IU CINF Flash session - ACS National Meeting, March 25, 2012 – San Diego, CA
- 2. Alternate title (and take home message): Cheminformatics is so great! But is it too good to be (transferably) true? 2 / 17
- 3. How great is cheminformatics? Example: Are these the same or different molecules? 3 / 17
- 4. How great is cheminformatics? Example: Are these the same or different molecules? Answer: Same, that’s easy, just use canonical graph algorithm via canonical SMILES: CNC1C(O)C(O)C(CO)OC1OC2C(OC(C)C2(O)C=O)OC7C(O)C(O)C(NC(=N)NCNC(=O)C4=C(O)C(C3CC6C(=C(O)C3(O)C4=O)C(=O)c5c(O)cccc5C6(C)O)N(C)C)C(O)C7NC(N)=N (TETRACYCLINOMETHYLSTREPTOMYCIN) 4 / 17
- 5. Thanks to… ? ? 5 / 17
- 6. Thanks to… Harry Morgan Dave Weininger Actor, “MASH” Daylight (Hmmm…?) (SMILES) / 17 6
- 7. Thanks to… Harry Morgan Dave Weininger ACS CAS Daylight (Morgan Algorithm) (SMILES) Et al., et al…. 7 / 17
- 8. Now about those proteins… • Example: Are these the same or different proteins? 1YIN: ALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEI LMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTL KSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA HRLHAPTS 3OS8: SNAKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTRHDQ VHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLN SGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVP SYDLLLEMLDAHRLHAPT PAM250 alignment score: (gap: -3; extend: -10) 1156 (1156/1260 = 92%) Ergo, um… Maybe. 8 / 17
- 9. Now about those proteins… • Example: Are these the same or different proteins? Answer: Same… but what does that even mean? 9 / 17
- 10. Why protein identification is hard • Proteins are large, complex, dynamic • PDB is database of crystallography experiments, not molecules • Ligands, co-crystals, waters • Protein crystallography & NMR is hard • History, culture… 10 / 17
- 11. How about human identification? (Should be easier, may shed light…) 11 / 17
- 12. Human identification hard too, apparently… Credit card fraud Homeland security http://forms.cybersource.com/forms/NAFRDQ12012whi 12 / 17 tepaperFraudReport2012CYBSwww2012
- 13. (Which brings us to…) My address book problems How many Rob Yangs? 13 / 17
- 14. (Philosophical tangent:) Are human entities actually identifiable? One Harry Morgan or two? How can we know? 14 / 17
- 15. (Philosophical tangent:) Are human entities actually identifiable? Individuality may be contextual. One Harry Morgan or two? How can we know? 15 / 17
- 16. Could I organize my address book using cheminformatics? What would the algorithm look like? 16 / 17
- 17. Conclusions • “CINF” (cheminformatics) is awesome. • But some CINF-awesomeness is not readily transferable to other domains. • Cannot automate logic if not logical (How many Harry Morgans?). • Perhaps CINF-awesomeness can be used as an indexing approach for chem-related domains. “Chester” 17 / 17