Questions tagged [pdb]

A file format used in structural biology to describe the 3-D coordinates of atoms of a biological structure, often a protein. Can also refer to the Protein Data Bank database, which stores all the submitted biological structures, most of which were obtained using X-ray crystallography.

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3
votes
2answers
151 views

How to find/build the evolutionary history of a protein from its sequence?

I aim to build the evolutionary history of a protein. For example given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein for example: ...
4
votes
3answers
301 views

Best distance parameter for estimating physical interaction between residues in a PDB file

We can calculate the distance between residues in a PDB file regarding different parameters like closest atoms, alpha carbon, beta carbon, centroid and etc. Which one of these parameters are better to ...
9
votes
4answers
606 views

Converter between PDB or mmCIF and MMTF

I'd like to test MMTF, a new format for storing biomolecular structures which is promoted by RCSB as a more compact alternative to mmCIF and PDB. From MMTF FAQ: How do I convert a PDBx/mmCIF ...