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This an initial solution, but can be improved: out = system2("f:/stride/stride.exe", "f:/stride/1a11.pdb -h", stdout=T) nh = strsplit(out[grepl("HBT", out)], " ")[[1]][2] print(nh) # Output: 26 (hydrogen bonds) I compiled an Windows version of Stride and uploaded here: http://lcrserver.icmc.usp.br/~daniel/bin/stride.exe


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This is a general answer for all three of your related questions: This one How does Temperature influences the rate of protein turnover? How is the rate of transcription influenced by temperature? Since you said: I want to simulate the evolution of genetic architecture when after a sudden change in temperature or in an environment that is ...


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The number of hydrogen bonds cannot actually be said from software only inferred. But you could try using STRIDE (http://structure.usc.edu/stride/) which takes the file name with a -h flag to output the number of hydrogen bonds. You could then write a small shell script which would pass in each file and store the data you wanted in whatever format you liked. ...


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The simple answer is that there are literally thousands of chemical reactions (mediated by enzymes) going on in the cell. Some produce H2O, others consume it. For example, when proteins are broken down into their individual amino acids as part of normal turnover in the cell, a water molecule is necessary to break the peptide bond. Therefore, the overall ...


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STRING is one available tool http://string-db.org/ and allowes you to do multiple sequences/names. I would also take an indepth look at what expasy has to offer http://www.expasy.org/proteomics. It is a large collection of bioinformatics tools (far too many for me to go through) and almost always has the tool you want. (As a side note Expasy also has tools ...


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Go to the NAR database site and look for protein domain databases. You have multiple options. Here is the link.


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Hydrophobicity means aversion to water which results because of increase in entropy of the system due to the water-"solute" interaction. As already pointed out in by inf3rno, polarity of a molecule is because of its net dipole moment. It is true that polar molecules can dissolve in water (because they can interact with water via van der Waals' forces ...


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The most important role of this peculiar double helix structure of DNA is to facilitate replication....in preparation of cell division each of the 2 strands acts as a template thus facilitating precise copying of genes....in the Nature(1953), Watson & Crick also suggested that " It has not escaped our notice that the specific pairing we have postulated ...


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The structure allows for the DNA to be tightly packed into chromosomes. It also provides an extremely stable backbone with the negatively charged phosphates pointing to the outside of the molecule. This charge aids in the attachment of other molecules to the strand of DNA. DNA double helix allows it to be stable and it won't easily destroyed.


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I investigated the topic too, so here is my answer. To understand thermodinamic stability of water solved globulins or membrane proteins (all of them proteins hereafter) we have to understand protein folding. Proteins have a 3d structure (composed by their primary, secondary and tertiary structures). The structure of the proteins is constantly changing ...


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Hydrophilic means attracted to water, while polar means the molecule has electric pole(s). A hydrophilic molecule or portion of a molecule is one that has a tendency to interact with or be dissolved by water and other polar substances. wikipedia - hydrophile A polar molecule has a net dipole as a result of the opposing charges (i.e. having ...


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You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as PhosphoSite. To get the actual modified residues, click on "PTM/Processsing" (sic) further up the page and then select "Modified Residue", and in your results table you'll get a list of all phosphorylations, glycosylations, ...


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Every amino acid has a different isoelectric point: a pH where they do not carry electric charge. This isoelectric point depends on the side chains: By glycine the side chain $-H$ is neutral (while the amino and carbonic acid groups are not) so the IEP is 5.97. By lysine the side chain $-(CH_2)_4\mbox{-}NH_2$ is alkaline $[R\mbox-NH_2 + H^+ ...


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First, when asking about a specific small term, it's best to check your spelling. If you actually look at the sentience, you will note that you left out a very important hyphen: Pellequer compared several propensity scale methods using a dataset of 14 epitope-annotated proteins. [emphasis added] The phrase means that the protein sequences (amino ...



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