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marcin's user avatar
marcin's user avatar
marcin
  • Member for 7 years
  • Last seen more than a month ago
7 votes

What is the aim of insertion codes in the pdb file format?

7 votes
Accepted

What does the yellow mean in this image from Virus Pathogen Resource?

6 votes
Accepted

What is the function of the heteroatoms

4 votes
Accepted

Algorithm for counting neighbors

4 votes
Accepted

CCP4 file to a Python 3 numpy array or similar workaround

4 votes

How to get all PDB homologs from Uniprot (mapping + BLAST)?

4 votes

How to extract RNA sequence and secondary structure restrains from a PDB file

3 votes

Biopython: resseq doesn't match pdb file

3 votes
Accepted

Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

3 votes
Accepted

Proteins with one SS bond?

3 votes

How many entries in PDB have SS bonds?

3 votes
Accepted

How to get 2d/3d structural coordinates from a PDB file?

3 votes

How to extract subset of protein structure (PDB format) file based on a subsequence of that protein

2 votes

BinaryCIF vs MMTF formats, which one to choose?

2 votes

How to extract part of protein complex separated with HEADER with two molecules from one PDB file

2 votes

How to extract subset of protein structure (PDB format) file based on a subsequence of that protein

2 votes

Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?

2 votes
Accepted

How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?

2 votes

What are the differences between "Site" and "CONECT" in a PDB file

2 votes

Can you query the RCSB PDB API with a ligand and return the IDs of all entries in which it appears as a free ligand?

2 votes
Accepted

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

2 votes

Cross-reference with PDB database

1 vote
Accepted

getting KeyError on certain residues in BioPython: ATOM vs. HETATM lines

1 vote
Accepted

What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?

1 vote

How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?

1 vote

Protein PDB/CIF text file reader that can fold a same section into one line

1 vote

PDB format: remark number for free text

1 vote

Downloading a list of all RCSB-PDB entries

0 votes

Get a list of PDB ids from a list of sequence protein number?

-1 votes

Reconstruct a protein's 3D structure from a pair-wise distance matrix