Podcast #128: We chat with Kent C Dodds about why he loves React and discuss what life was like in the dark days before Git. Listen now.
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These illustrations are by David Goodsell, and carry his famous look. Whilst I was not able to determine what specific software he uses, this page suggests that he probably creates his illustrations as a composite of renders and that the outlines and depth cueing are achieved by running a 'find edges' filter over the z-buffer of the scene, which can be ...


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One example of disastrously different effects of very similar molecules is thalidomide. There are two isomers, only differing in their stereochemistry. The (R)-isomer is responsible for the sedating effect it was initially used for. The (S)-isomer lead to horrifying birth defects in the children of woman that took that drug. It is somewhat more complicated,...


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trb456 and Mad Scientist have raised the point that enantiomeric forms of a bioactive molecule may have markedly different activities, however there's more to it than that. A molecule that has a similar shape and surface charge distribution to another biologically important molecule is liable to bind to the same protein receptor sites, but in different ways. ...


15

The $\ce{Fe}$-porphyrin complex is a vastly conjugated $\pi$-system, in which the oxidation state of the $\ce{Fe}$ plays a central role. The wavelength of light absorbed by hemoglobin exactly corresponds to the the difference in energy between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the heme $\pi$-...


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I (accidentally) stumbled upon the following statement in Atkins' "Elements of Physical Chemistry" (p378): We represent dipole moments by an arrow with a length proportional to $\pmb{\mu}$ and pointing from the negative charge to the positive charge (1). (Be careful with this convention: for historical reasons the opposite convention is still widely used.)...


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I am not an expert in the field, but a quick literature check turns up a good amount of papers on the topic. In particular, I found this paper [1] which nicely answers the question for guanine: So, in the gas phase, the most stable enol tautomer has a 0.9 kcal/mol free energy difference with the most stable keto tautomer. That free energy difference is very ...


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None of the chemical file formats are typically accepted by 3D printing services. The reason is that chemical file formats are fundamentally different from those describing 3D objects. In the simplest case, a chemical file format describes a list of atoms and their positions (plus possible metadata). An example is the XYZ format, which stores exactly that. ...


9

Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \vartheta_\mathrm{opt} < 80~\mathrm{^\circ C}$) and hyperthermophilic ($\vartheta_\mathrm{opt} \approx 100~\mathrm{^\circ C}$) organisms compared to homologous ...


9

There's several aspects to your question. Does quantum mechanics play a role in protein folding? Yes. The origin of the van der Waals interaction is ultimately a quantum mechanical one. (At least the induced dipole portions: how the electrons move with respect to each other and an external electrical field is driven by quantum mechanics.) Also, while part ...


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Macromolecular NMR spectra are difficult to compute because macromolecular electronic structures are computationally expensive to solve with accuracy. Obtaining precise chemical shifts and splitting requires accurate treatment of electron density and geometry, especially for simulation of NOESY, which I understand is important in macromolecular structural ...


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Let's take a simple case of a positive charge $q_+$ and a negative charge $q_-$ with $q_+ + q_- = 0$ placed along the $x$-axis at $x_+$ and $x_-$, respectively. The dipole at the $x=0$ is $$\mu=q_+x_+ + q_-x_- $$ which can be rewritten as $$\mu=q_+(x_+ -x_-) $$ which is a vector pointing from $x_-$ towards $x_+$. So this is the "natural" direction based on ...


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UPDATED: I wrote a first answer assuming that $t>0$ which got close to what's in the paper, but not quite the same. Thanks go to Karsten Theis for pointing out that $t<0$ in these "backward equations". Here's a corrected explanation: The scenario is that we have a system that can be in any of seven consecutive states (numbered 0 through 6). At some ...


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I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer. Generally the structure is similar... Comparison of many nuclear magnetic resonance (NMR) solution structure ensembles with crystallographic structure has shown that the core structure of protein molecules remains unchanged compared with the solution state during ...


6

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. First note that, in principle, for the time being, quantum mechanics is considered to be universally valid at all size and time scales. So, in general, it does not really matter how big a system is or how long a process takes: every system is a quantum ...


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There is a paper on bolaamphiphiles (1) where it is stated that measured surface area corresponding to the area of a bixin molecule lying on the water surface with most methyl groups pointing outside is approx. $\pu{1.0 nm^2/molecule}$ at zero pressure. If the methyl groups were parallel to the water surface, a molecular area of approx. $\pu{1.7 nm^2/...


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I was curious to see what kind of research had been done on this topic, and didn't expect to find much, but I was quite wrong. So, I'll summarize some articles that I found and give the references at the bottom. Why would we ever consider quantum mechanics in protein folding? First, an introduction to why someone would even try to come up with a quantum ...


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I did some work on interpreting neural network QSAR models - I won't claim that they explain everything and has a number of limitations (linearizes network connections, applicable only to feed forward networks). But maybe it will be useful Interpreting Computational Neural Network QSAR Models:  A Measure of Descriptor Importance Interpreting Computational ...


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Since you are interested in Artificial Neural Networks that also explain their decisions/predictions you may be interested in transparent neural networks, although they have not been used to my knowledge on chemical information. Other interesting approaches include inductive logic programming which have among other things been applied to predicting binding ...


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One way to do it is to perform a quantum chemistry calculation of the electrostatic field generated by the molecule. Another is to determine (or assume) partial atomic charges for each of the atoms of the system, and use a Poisson solver (as I believe APBS is) to calculate the electrostatic field generated by this point charge distribution.


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In biochemistry branch searching for new drugs, it was common to search for new active substances using chemical similarity. It does have reasoning behind it. Most drugs acts, binding themselves to some protein site, in the place, where normal ligand of the protein will bind. However, chemical similarity is not enough to be a drug. Sure, a substance must ...


4

There are several kinds of snake venom, and as far as I know they are all complex enzymes: it means that they are complex macromolecules, made by amminoacids (these, "small molecules") bound with peptide bonds. For enzymes and proteins, the chemical nomenclature is quite impratical: it's way easier to define the enzyme by giving the names of the amminoacid ...


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Are all the biochemicals that our body uses enantiomerically pure or are racemic mixtures too? Many molecules exist in both forms in nature. One fun example are the enantiomeric terpenoids R-(–)-carvone and S-(+)-carvone. The R-form smells like spearmint while the S-form smells like caraway. The difference in smell shows that properties other than the ...


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Just browsing through this "Unanswered Question" now (in late 2014). I hope it's not too late? In protein structure validation, Ramachandran outliers are a strong, but not absolute, indicator that the backbone confirmation of your protein structure deviates from all the high resolution structures known to date, and hence need your attention during the ...


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The data provided by @F'x are very helpful towards answering the question. But the relative stabilization of the bases when hydrogen bonded to each other is germane to the question. Because the role of stacking is still being worked out, I don't think this question has a simple answer. Since wobble pairs are observed, but I haven't seen them outside a ...


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DNA is not a protein, as @MARamezani states. See http://www.answers.com/Q/Is_DNA_a_protein. There is a prevalence (or lack) of some amino acids in certain sources. For example, maize ("corn" in America) is deficient in tryptophan and lysine, so if your sample is short on those two, it is more likely that it is from corn. A list of some foods and amino acid ...


3

Yes it is true that protein folding takes a long time compared to bond vibrations (few femtosecond) or rotations of a amino acid (picoseconds to nanoseconds) and for small proteins can take of the order of a few tens of nanoseconds. Typically proteins with many amino acid residues, say 100, this time can reach to microseconds and seconds and in fact cannot ...


3

I am sure that a more definitive answer could be provided by someone more familiar with the field, but here are a couple of observations. First, I think it is a bit of an exaggeration to say that protein folding is almost entirely the result of entropy because the protein will have larger entropy in the unfolded state than in the folded state. The main ...


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Try DNA origami instead While protein assemblies are well known, rationally using proteins to assemble larger supramolecular structures is still a difficult problem: Predicting protein folding is an unsolved problem. Sometimes even small modifications to a sequence can change the folding propensity. Predicting protein-protein interactions is often ...


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So how are the cells are arranged to form a solid structure a solid body? Plant cells have cell walls, are filled with liquid, and have strong cell-cell adhesion. This gives a fairly rigid structure that may seem like a solid. Take a carrot for example, it seems solid. But if you put the carrot in a blender, you get carrot juice - not a solid. Also, when ...


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