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There is a recent paper that introduced the first molecular-level whole-cell simulation.
Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044
The ...
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At the MEME server page, there's a link to upload a customized background markov model (using the command line interface, this is the -bfile option). From there, there's a link to the MEME Man Page. Under "Objective Function", it specifies:
The background model is an n-order Markov model. By default, it is a 0-order model consisting of the ...
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There is a lot of variation in how and when deer shed their antlers. In most arctic and temperate-zone species, antler growth and shedding is annual, and is controlled by the length of daylight. In tropical species, antlers may be shed at any time of year, and in some species such as the sambar, antlers last several years. Some equatorial deer never shed ...
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Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt ...
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I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds.
Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,
jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS")
Step 2: Only display the hbonds
jmolScriptWait("display connected(hbond)")
Step 3: Export the ...
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I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go ...
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I think that you could try a similar approach to GSFS:
use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene)
use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..)
divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order ...
2
What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
One application that I am aware of that will do this, as well as much else besides, is Swiss-PDB Viewer aka DeepView. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.
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http://www.turbosquid.com/3d-models/max-human-brain/580672
That one is only 30 which really isn't bad for a model. You will have trouble finding an anatomically correct model for free.
I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? ...
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The Open Source Computer Vision library OpenCV is pretty popular. I'm a Python guy, but it also has C, C++, and Java interfaces. The O'Reilly book Programming Computer Vision with Python was pretty good, and their C-oriented Learning OpenCV from 2008 is coming out with a new C++ edition in July, supposedly. There are also the OpenCV online docs, linking to ...
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What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
Visualising the change induced by an amino acid on the 3D structure is part of an entire field of research call molecular modelling (http://en.wikipedia.org/wiki/Molecular_modelling). There is a huge body of research available on the subject and I am not up-to-date anymore in this field.
What I used to do was simulating the optimal shape of a AA chain (~10) ...
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I searched a bit and could not find any such format, but I am not a specialist in taxonomy.
From what I understand, the structure you want is that of either a tree or a DAG (Directed Acyclic Graph). Both are straightforward to store in a variety of formats.
One possibility is to use a format similar to other biological data that has a similar data ...
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Try this one
Pavel, A. B. & Vasile, C. I. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics 13, 9+ (2012).
You can download here
http://sourceforge.net/projects/pyelph/
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I'd like to add regulonDB which is not as integrated, but has a tremendous map of the e coli regulome which would be useful for any bacterial model.
I agree with @DanielStandage that this is not a well understood and there don't even appear to be standard representations for this sort of data.
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