Hot answers tagged

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.


10

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 ...


7

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 ...


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

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 ...


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

The flat arrows are a cartoon representation of β-strands (one type of regular hydrogen-bonded secondary structure). The direction of the arrow is the direction of the amino acid sequence (arrow head pointing towards the C-terminus). The thin wires are regions with no regular structure. There are also two small green spiral ribbons in the foreground left ...


3

If what you are after are the structural co-ordinates of particular amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should find them along with other small molecules in the Cambridge Structural Database.


3

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 ...


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

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 ...


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 ...


3

There is a model of an adult, male, real human brain here: http://brainder.org/download/brain-for-blender/ It can be imported into Blender or any other 3D application that can read Wavefront OBJ or Stanford PLY formats.


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

I'm resurecting an old question, but I've heard this question from a few young bioinformaticians and had a couple more points to consider about compressing PDB files. The first is that many PDB files (including all PDBs hosted on the PDB site) have some 300-400 lines of meta data at the top of the file. This accounts for about 10-20% of the total file ...


2

Unfortunately it is impossible to predict the tertiary structure of proteins using raw amino acid sequence. The information required to be computed in the construction of the dynamic protein shape is too large for any computer at the moment. There are actually a list of research facilities that are looking for people to donate their computer's idle CPU ...


1

So, after the restriction digestion, the sample consists of DNA fragments with 5' overhangs. These are filled in by Klenow DNA polymerase, adding biotin-dCTP to both ends of each fragment. Then the fragments are ligated under conditions (ie low DNA concentration) such that ligation between non-crosslinked DNA is less likely. This reduced ligation efficiency ...


1

Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary ...


1

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


1

I think all models are too generic out there. Radiological models you can find in imaios.com's e-Anatomy where the Premium access gives you some RTG, CT and MRI videos which you can combine to form some 3D models. I am working with the visualization of CNS lymphatic vessels here where I would like to create thin membranes to visualize how deep the ...



Only top voted, non community-wiki answers of a minimum length are eligible