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5 votes

Can two protein secondary structures "overlap" in the PDB?

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary ...
James's user avatar
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5 votes
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How can I evaluate the hydrophobicity and/or surface charge of a protein?

Since you have the structures the best option, in my opinion, is Pymol. Hydrophobicity Open Pymol. Load up your protein of choice. Download color_h.py which is a script from the University of Osaka ...
James's user avatar
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5 votes
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How to filter out the antibody light chains into kappa and lambda types on the PDB website?

The instructions are as follows. Go to the RCSB PDB Webite. Under the search bar, click Browse by Annotations. Click the blue tab labeled ...
mpprogram6771's user avatar
3 votes
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Transformation of coordinates found in PDB

The purpose of these matrices is to reconstruct the crystal lattice from the coordinates, which only contain one copy of the repeating structural unit found in the crystal. In other words, they ...
biohacker's user avatar
  • 409
3 votes
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How is the "global pLDDT" score in the Protein Data Bank calculated?

pLDDT is a measure of confidence that ML models like AlphaFold provide for predictions of protein structures. The entries you are sorting here are not predictions, they are all experimental structures....
timeskull's user avatar
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3 votes
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Why do chain identifiers in PDB have no standard starting chain id type?

Chain IDs are assigned by authors who submit the structure to the wwPDB. According to the PDB spec: Non-blank alphanumerical character is used for chain identifier. Usually, the chains are ...
marcin's user avatar
  • 449
3 votes
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How many proteins on PDB have unknown function?

The article cited in the question indicates that the authors searched the PDB with the term “unknown function”. There is nothing special about this — you just type in the standard search field and hit ...
David's user avatar
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2 votes

How to edit manually pdb structures?

If I remember correctly pymol can edit pdb structures (as well as visualize them). I've used a student version though (which is a free full version) and I'm not quite sure if its possible to use ...
Nicolai's user avatar
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2 votes
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Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

It seems that if no HELIX record is present in the PDB, PyMol attempts to assign secondary structure itself. For whatever reason, it does not do this if multiple <...
canadianer's user avatar
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2 votes

How can I evaluate the hydrophobicity and/or surface charge of a protein?

I think you are after protscale. It gives you a whole bunch of options to predict how your protein will be 'behave' for HPLC purification and hydrophobicity, buried residues, etc.
mimat's user avatar
  • 1,425
2 votes

How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

Your approach is correct but it is worth considering which database will work best for you. Questions to consider are; Does the database provide a large search space for the organism(s) you're ...
Michael_A's user avatar
  • 1,305
2 votes

Compressing structural information in PDB files

I know the question is old, but for the record: the RCSB PDB is currently working on a project to compress the PDB structural data with a new file format, called MMTF (MacroMolecular Transmission ...
Jose Duarte's user avatar
2 votes

Relationship between an Integrin-binding peptide and the Collagen type that it models

Summary The entry for 4BJ3 on the web pages of RCS Protein Data Bank contains information regarding a “collagen-like, GFOGER peptide” (authors’ words) that is at the best misleading and at the worst ...
David's user avatar
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1 vote
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How do I identify the carbonyl atoms in a PDB file

Looking at the ATOM records for an Ala residue, as an example: ATOM 132 N ALA A 33 0.179 -33.349 1.978 1.00 18.93 N ATOM 133 CA ALA A 33 0.316 -32.425 0.863 1....
canadianer's user avatar
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1 vote
Accepted

How can I extract ligand with neighboring protein atoms from PDB with complex?

You might find RCSB's Guide to Understanding PDB Data and the PDB file format documentation useful. I'll go over some of the information present in PDB files that seems relevant for you, using your ...
canadianer's user avatar
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1 vote

Relationship between an Integrin-binding peptide and the Collagen type that it models

I checked ENSEMBL and the reason is not due to known alternative splicing but still allows for the possibility that they investigate a different sequence/allele due to mutations. Importantly, in the (...
KaPy3141's user avatar
  • 1,597
1 vote

Structure coordinates in PDB file

The atom numbered 1 in a PDB file is the most N-terminal atom visualized by the structure determination — the most N-terminal amino acid, the co-ordinates of which are presented. If the X-ray ...
David's user avatar
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