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Questions tagged [protein-structure]

The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.

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Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?

Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations. Specifically helping screen existing drugs against ...
Paul Shen's user avatar
8 votes
2 answers
261 views

Getting structure and sequence related to PDB IDs

I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer. In a heterodimer there are two chains ...
Sara's user avatar
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2 votes
1 answer
167 views

Generate ligands candidates based on protein shape

Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
Jim Eric Skogman's user avatar
1 vote
1 answer
297 views

Extract autodocked protein-ligand connections programatically

I have 2 crystal structures, one for my protein and one for my ligand (I have several protein-ligand pairs). I am using AutoDock Vina to simulate docking, which returns another file of the ligand with ...
Zac R.'s user avatar
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10 votes
5 answers
10k views

How can we find the distance between all residues in a PDB file?

If we have a PDB structrure, how can we find residues physically interacting with each other in space? I know that we must find the distance between residues and if the distance is less than 5-6 ...
Sara's user avatar
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8 votes
2 answers
956 views

Phyre2 vs ITasser, completely different models generated

Does anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am ...
Te-Yo's user avatar
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7 votes
3 answers
2k views

Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

As the title summarizes, I am trying to: Read a PDB file (for example, 1enh.pdb). Extract the backbone dihedral angles (phi, psi). Modify the dihedral angles (phi, ...
epsilone's user avatar
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5 votes
3 answers
2k 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 ...
Sara's user avatar
  • 777
5 votes
2 answers
250 views

Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
CubeHead's user avatar
  • 425
4 votes
1 answer
3k views

How to quickly and robustly convert between mmCIF and PDB?

There is already a question on PDB/CIF to MMTF, however what is a robust way to programmatically go between PDB and CIF files? For example I can use a python script from this gist that relies on ...
James's user avatar
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2 votes
1 answer
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How reliable is Alphafold2 for folding random-coil peptide

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
neversaint's user avatar
1 vote
1 answer
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How to calculate RMSD and binding energy from the already docked ligand-receptor

I have the following PDB file that looks like this. It is downloadable here. This PDB already contains ligand and receptor together. The red molecule is the ligand and the yellow is the receptor. They'...
littleworth's user avatar
1 vote
1 answer
133 views

Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)

I am running rosetta ab initio prediction using the command line: ...
DanielSebas's user avatar
1 vote
2 answers
238 views

DMPfold error while running protein structure prediction

I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between: ...
DanielSebas's user avatar
0 votes
1 answer
215 views

How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?

Suppose, I want to find the neighboring Hydrogen atoms of a specific C-alpha atom. The following was my effort. However, it produces a bunch of empty lists. ...
user366312's user avatar
-2 votes
1 answer
218 views

Are there any Sulfur Dioxide molecules in this structure?

Does the protein structure shown in the JSmol link have any Sulfur Dioxide molecules? In the picture, the Sulfur element is yellow and Oxygen is red (see here) https://www.viprbrc.org/brc/...
Andy's user avatar
  • 153