13 posts · 1,646 views
This blog are about articles in the field of Structural Bioinformatics that I found interesting and wanted to write a short description about them, so that others might find it interesting as well.
This is not a regular research blogging post, but important enough that anyone following this blog should be aware of it. Most of you doing research, I assume being associated with an institute/university, would have an academic email id that does not end with .com. You are vulnerable, my friend. Yes, the subject is "open access publishing scam".... Read more »
Butler, D. (2013) Investigating journals: The dark side of publishing. Nature, 495(7442), 433-435. DOI: 10.1038/495433a
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Almost all of us visiting PDB would have looked at the image shown below that attract us like moths attracted to a light. I am talking about the aesthetically pleasing protein images created by David Goodsell. In case you didn’t know, he is the author of Molecule of the Month series. Since the images look anything like the ones we usually keep looking at, one is attracted to the level of abstraction the image projects due to which, the reader understands the big picture. And, of course, th........ Read more »
Sanner MF. (1999) Python: a programming language for software integration and development. Journal of molecular graphics , 17(1), 57-61. PMID: 10660911
Sanner MF, Olson AJ, & Spehner JC. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38(3), 305-20. PMID: 8906967
Recently, Babel (in my system) was not working and I needed to convert my .sdf files to smiles format. I troubleshooted the error was able to run successfully. But, this made me think, what about a web-based application to do this format conversion? That's how I found these three amazing tools based at the National Cancer Institute's CADD Chemoinformatics group.... Read more »
Weininger, D. (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Modeling, 28(1), 31-36. DOI: 10.1021/ci00057a005
I have encountered this issue while working with structures in PDB that are solved using Nuclear Magnetic Resonance (NMR). Which model should I choose among the 10 or 20 models? As a general rule of thumb, Model 1 is usually taken for further analysis and consideration. Is that rule universal for all NMR structures? Some studies on this topic makes it interesting to revisit.... Read more »
Sutcliffe, M. (1993) Representing an ensemble of NMR-derived protein structures by a single structure. Protein Science, 2(6), 936-944. DOI: 10.1002/pro.5560020607
MacArthur, M., & Thornton, J. (1993) Conformational analysis of protein structures derived from NMR data. Proteins: Structure, Function, and Genetics, 17(3), 232-251. DOI: 10.1002/prot.340170303
Laskowski, R., Rullmann, J., MacArthur, M., Kaptein, R., & Thornton, J. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4). DOI: 10.1007/BF00228148
Gottstein, D., Kirchner, D., & Güntert, P. (2012) Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. Journal of Biomolecular NMR, 52(4), 351-364. DOI: 10.1007/s10858-012-9615-8
So, here is an imaginary situation. You have a deadline to achieve and have minimal internet to reach the goal. Few hours before the deadline, your PI asks if you can send him a movie of the protein of interest in PyMOL. He specifies that the movie show the protein rotating, the active site and the ligand bound with it in surface representation, ligands as ball-and-stick, etc. He has a grant review presentation tomorrow and needs it asap.
You finish the movie and realize that to make a good i........ Read more »
Porollo, A., & Meller, J. (2007) Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics, 8(1), 316. DOI: 10.1186/1471-2105-8-316
Just like Multiple Sequence Alignment (MSA) tools there is a definite need for multiple structure alignment tools. For a long time, I was a big fan of Combinatorial Extension (CE)'s Multiple Structure Alignment (MStA) on their web server. Now, it is no longer maintained and has become a legacy. The good thing about it was you can do pairwise, database search, and MStA by either giving the PDB id or uploading a file.... Read more »
How can Molecular Dynamics help in controlling pests? Well, insects have something called resistant to dieldrin receptor or RDL receptors. These are part of a big family of receptors called Cys-loop receptors. Insecticides invariably bind to these receptors and in turn affect the neurotransmission in the pest. So, it becomes imperative to understand these receptors in order to develop and rationally design insecticides that are highly specific.... Read more »
Ashby, J., McGonigle, I., Price, K., Cohen, N., Comitani, F., Dougherty, D., Molteni, C., & Lummis, S. (2012) GABA Binding to an Insect GABA Receptor: A Molecular Dynamics and Mutagenesis Study. Biophysical Journal, 103(10), 2071-2081. DOI: 10.1016/j.bpj.2012.10.016
post about special feature on protein folding in PNAS, October 2012 issue... Read more »
Wolynes, P., Eaton, W., & Fersht, A. (2012) From the Cover: Chemical physics of protein folding. Proceedings of the National Academy of Sciences, 109(44), 17770-17771. DOI: 10.1073/pnas.1215733109
2D representations for protein-ligand interactions... Read more »
Wallace AC, Laskowski RA, & Thornton JM. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering, 8(2), 127-34. PMID: 7630882
Stierand, K., & Rarey, M. (2010) Drawing the PDB: Protein−Ligand Complexes in Two Dimensions. ACS Medicinal Chemistry Letters, 1(9), 540-545. DOI: 10.1021/ml100164p
Durrant, J., & McCammon, J. (2011) BINANA: A novel algorithm for ligand-binding characterization. Journal of Molecular Graphics and Modelling, 29(6), 888-893. DOI: 10.1016/j.jmgm.2011.01.004
Post about the distinguishing omega loop that gives rise to substrate specificity in cellulases.... Read more »
Sukharnikov, L., Alahuhta, M., Brunecky, R., Upadhyay, A., Himmel, M., Lunin, V., & Zhulin, I. (2012) Sequence, structure, and evolution of cellulases in the glycoside hydrolase family 48. Journal of Biological Chemistry. DOI: 10.1074/jbc.M112.405720
Post about a paper that says those residues in a protein that show least mobility (relative to others in the same protein) are most likely to be conserved... Read more »
Liu, Y., & Bahar, I. (2012) Sequence Evolution Correlates with Structural Dynamics. Molecular Biology and Evolution, 29(9), 2253-2263. DOI: 10.1093/molbev/mss097
An early post on seminal work by Jane Richardson... Read more »
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