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17

6405 proteins mapping to 5220 genes, according to Ensembl. In Ensembl's BioMart, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.


9

PDB is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins: Open Advanced search tab of the PDB website. Select Biology -> Source organism from the menu. Type Homo sapiens (human). You can reduce redundancy by checking Remove Similar ...


6

Yes, nucleosomes are completely unwound. Histone chaperones such as FACT (for H2A/H2B) and ASF1, CAF-1, HIRA, Nucleophosmin etc (for H3/H4), associate with RNA Pol II and handle the displaced nucleosomes. As you surmised, the histone octamer complex is disassembled, into the H3/H4 tetramer and two H2A/H2B dimers. Right behind the elongating Pol II, the ...


5

I think the picture will help you. In fact, to determine which kind of rearrangement for the chromosomal, we need to define an "orientation". However, this orientation is not fixed. It is a definition compared with the two chromosomes before and after the rearrangement. As the picture shows, the duplicated sequence after rearrangement should be in the same ...


4

There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised. Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed ...


4

You are making a few assumptions that are likely not valid for all PDB files. For example: Residue indices are not necessarily sequential, nor do they have to start at 1 Not all possible residues have 1-letter code equivalents, there are thousands of possible exotic residues, not only the standard amino acids PDB files are not only used for proteins, but ...


3

First of all: Honey is not a byproduct of bees - it's their main and most important product which stores energy for the bee hive for the time when no flowers are available. Honey itself consists (according to the USDA database) to about 99.5% of water and sugars (82.5% sugars, 17% water). The sugars are mostly fructose and glucose, but also some other mono- ...


3

The PDB file format was specified in the dawn of computing to fit on punch cards. So it has some shortcomings that have led to generations of scientists cursing the fixed-width column format. By now, it has been superseded by an XML-like format: PDBML. Of course XML is less space-efficient than a column layout, so you can see that disk space was not the main ...


3

From your comments it doesn't seem like you are adverse to writing some custom scripts so one option would be to take advantage of the NCBI Structure database. You can filter it by organism and then download the results as a text file / XML. If you need access to the raw PDB data you could then download the PDB archive and examine the ones in your filtered ...


3

The only paper I found that examined the question is "Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases". They state The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most ...


2

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? ...


2

A 3D model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic or aniosotropic B-factor (that models atom fluctuations). A '1D' SMILES is not a physical 1-dimensional representation, and can be converted to a graph ...


1

3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


1

only a small peptide of Osteopontin is available currently http://www.rcsb.org/pdb/protein/P10451



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