Questions tagged [3d-structure]

The spatial organization of atoms within a macromolecule.

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How many proteins on PDB have unknown function?

I was wondering how many of the files in the Protein Data Bank (PDB) have unknown function. The only paper I can find from an internet search is this one from 2012, which I assume might be outdated. I’...
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105 views

How to interpret this PubChem record of L-Alanine

Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule. Raw data here. I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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78 views

Automating figure-making with PyMOL

What I want to do I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
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18 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
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1answer
248 views

Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur? [duplicate]

I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands ...
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264 views

Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
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71 views

Please explain this notation MW around 9 MDa

I am a computational science student and was reading about the structure of Pyruvate dehydrogenase (PDH). link to article The article mentions "PDH is a large complex (MW around 9 MDa) consisting of ...
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Does any molecule other than DNA have a double-helical structure?

DNA is known to have a double-helical structure. Do any other molecules have this structure?
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2k views

How hard it is to determine a 3d structure of a protein?

I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and ...
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45 views

How can one determine how much of a region flanking an RNA sequence of interest to include in order to look for interfering secondary structures?

I have a set of RNA sequences, and I have been analyzing slices (i.e. target frames) of these sequences in order to determine whether they conform to certain structural criteria. One of these criteria ...
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99 views

Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
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2answers
181 views

Are there functional examples of parallel DNA double helices?

The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this ...
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69 views

At what point, when connected, do DNA strands become a helix?

When synthesizing DNA strands and beginning to "connect" them, how quickly does it become a helix? In this answer, canadianer says The helical structure is more stable than the "straight" form (...
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1k views

Twist in the DNA double-helix

DNA, has a deoxyribose sugar — phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base–sugar molecules are ...
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2answers
5k views

DNA topology Linking number vs twist?

Background Linking number: the linking number represents the number of times that each curve winds around the other. Twist, called "twist", refers to the number of Watson-Crick twists in the ...
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71 views

How to drop a grid of points in DICOM images of a CT scan (imageJ? Horos?)

I have a series of DICOM images from a CT scan of a bucket of rocks. I want to systematically measure the size of the interstitial spaces. The reason I'm doing this is to compare it to a simulation I'...
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3k views

What is the actual size of a nucleotide?

I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?
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102 views

How does RCSB determine the origin of the Cartesian coordinate system utilized in all PDB files

When perusing through the text version of a PDB file, I noticed in records that begin with "ATOM," there are x, y, and z coordinates for these atoms. How is the origin of each molecule's Cartesian ...
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2answers
489 views

Coordinates of amino acids in a protein sequence

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL......
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529 views

Meaning of arrows in 3D representation of proteins

Below is a three-dimensional representation of the protein, CD4. I would like to know what the arrows and the thin wires between them mean.
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2answers
83 views

Server for protein structure prediction for multiple sequences

Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, ...
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26 views

Where can one find completed and processed Hi-C datasets?

I and a statistics graduate student at UCR, and I am working on Optimal Binning schemes and peak detection in Hi-C data analysis (a dataset that conveys information about proximity of a DNA strand ...
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1answer
1k views

What happens after the purification step in Hi-C sequencing?

I am a statistician reading an article on Hi-C, and I am trying to better understand one of the steps in the DNA isolation and sequencing process. Since I'm a statistician, please try to avoid too ...
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197 views

How to use swiss-mod to predict the secondary structure and 3D structure of a protein?

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...
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379 views

Do nucleosomes ever completely unwrap during transcription?

In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.
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1answer
304 views

Simplified molecular-input line-entry system

This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer. What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is ...
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1answer
140 views

Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

I am interested in studying honey and other honeybee byproducts. I have not been able to find sequence or structure records for any of the contents of honey. In particular, I want to study the ...
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166 views

Clarification on the “orientation” of chromosomal rearrangements

I need some clarifications on the concept of "orientation" in case of chromosomal rearrangements. Given a deletion event on a chromosome for example, is the resulting DNA at the breakpoint always in ...
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2answers
261 views

PDB file for Osteopontin (SPP1)

I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself. Thanks
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4k views

What is the fibre axis in the Watson and Crick paper?

I was reading Watson and Crick’s original article on DNA structure in Nature 171, 737–738 (1953). The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. ...
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3answers
4k views

3D models of adult male brain in the Blender software? Any open-sourced version for research?

I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would ...
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1answer
128 views

What are the distinctive structural features of single- or double-stranded xRNA, or where can I find them?

I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form. I am ...
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4answers
697 views

Compressing structural information in PDB files

There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
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2k views

How many human proteins have a solved 3D structure?

I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.