bobthejoe

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PhD student in chemical engineering

	3,880 reputation	bio	website		visits	member for	1 year, 5 months
526 badges		location			seen	Jun 13 at 20:03

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Mar 4	comment	Is bootstrapping an acceptable way to determine standard error for binding constants? What is the definition of independent in this case? Does running a dilution series maintain independence? Now I'm even more curious how legitimate this is.
Mar 2	comment	Is there a binding affinity metric for interactions not in equilibria? Your basing your argument on psuedosteady state criteria and a constant concentration of your peptides and proteins. k_on and k_off are exclusively kinetic based terms that can be extended to thermodynamic terms when in equilibria which you're not in.
Mar 1	answered	Is there a binding affinity metric for interactions not in equilibria?
Feb 29	comment	What is the least costly method to generate sequential amino acid deletions? Also see openwetware.org/wiki/Preparing_chemically_competent_cells
Feb 29	comment	What is the least costly method to generate sequential amino acid deletions? Probably deserves its own question. The answer is yes. I don't know how many passages E. coli can go through before they lose their chemical competency. One of these kits can make a couple hundred of shots. zymoresearch.com/e-coli/transformation-kits-accessories/…
Feb 29	revised	What is the least costly method to generate sequential amino acid deletions? added 192 characters in body
Feb 29	comment	What is the least costly method to generate sequential amino acid deletions? I may be biased but there is an entire MATLAB toolkit developed for this exact purpose for highthroughput alanine scanning using overlap extension. The nice benefit is that your costs gets reduced to only 1 oligo rather than 2 oligo per mutant. simtk.org/home/na_thermo
Feb 29	comment	What is the least costly method to generate sequential amino acid deletions? I've always made my own competent cells (DH5alpha cells which is why I don't know the costs). I would assume that you would want to keep your vector in an expression strain so if you want to skip a step, I would transform straight into BL21.
Feb 29	comment	What is the least costly method to generate sequential amino acid deletions? If we're thinking about this problem from the context of traditional biochemistry, I would just have nothing. That is if your gene is XABCDEFGHY, you now have XY. You still have the context of the rest of the "gene" to observe. It should be a nice negative control.
Feb 29	answered	What is the least costly method to generate sequential amino acid deletions?
Feb 28	comment	How strong is spider silk? I hate to admit that wikipedia does pretty much answer this question. Followup question. What does it mean?
Feb 28	revised	Ideal low-protein binding membranes more details included
Feb 28	asked	Ideal low-protein binding membranes
Feb 28	asked	Is bootstrapping an acceptable way to determine standard error for binding constants?
Feb 28	asked	How does one calculate the resolution of a crystal structure?
Feb 28	asked	How strong is spider silk?
Feb 28	comment	Determining potential protease sites within a recombinant protein I should add that I've been using cell-free protein expression. However, the question at hand is completely independent of the expression system used.
Feb 28	revised	What is the molecular mechanism of cystine bond formation? changed the focus of the question.
Feb 28	awarded	Quorum
Feb 28	comment	Determining potential protease sites within a recombinant protein +1. Tried using the cOmplete tablets and still seeing problems. Do you have a good idea what's in the mix?