Questions tagged [structural-biology]

Questions relating to the structure (3-D conformation) of biological molecules, such as protein, RNA and DNA.

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Energy error margin for protein structures

I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
Omar Shehab's user avatar
2 votes
0 answers
21 views

(Complete) Stuctural Models of Antibodies: Combining Fc and Fab from pdb to Build Hinge Region? Or what?

I'm a newcomer to the field of antibodies, and I'm seeking guidance on obtaining 3D structures for my molecular simulations. After browsing the PDB databank, I noticed that there are Fab and Fc ...
LameSloth's user avatar
3 votes
1 answer
238 views

How to extract a list of hydrogen bonds from a PDB?

I am analyzing the 7VF2 structure, from the RCSB-database. I noticed that some residues belonging to one of its chains interact with the other chains that are present within the assembly. My question ...
Spartan 117's user avatar
3 votes
2 answers
94 views

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

I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a _entity_poly.pdbx_seq_one_letter_code...
rtviii's user avatar
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3 votes
3 answers
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What is the correct method of identifying the interacting residues for specific molecular docking?

I'm trying to do a specific molecular docking using Autodock Vina in PyRx. So, one way to do that is to mark all of the interacting residues and make sure the grid box encompasses all of that ...
Dembappe's user avatar
5 votes
4 answers
280 views

File I/O error using nglview.show_biopython(structure)

So I have been trying to get into visualizing proteins in python, so after some research I ended up on a tutorial that was teaching you how to visualize a protein from the COVID-19 virus, so I went ...
Jeremiah Wade's user avatar
2 votes
0 answers
167 views

Writing to .cif from BioPandas

My question is twofold. First, I've run into an issue working with .cif files and pandas dataframes. With BioPandas, I can read a .pdb file into a dataframe and then go the opposite direction, writing ...
Brookspj's user avatar
1 vote
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The difference between sequence-independent and sequence-order independent structural alignment?

I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is ...
fcan's user avatar
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How to analyze Circular Dichroism data? Best practices, typical approaches and so on [closed]

I have to analyze circular dichroism data of proteins and nucleic acids for my PhD. Despite I have been able to find vast literature that helps to interpret a spectrum, most of the papers describe ...
Spartan 117's user avatar
0 votes
2 answers
750 views

Pymol: select low confidence regions from AlphaFold pdb file

I have downloaded a predicted structure from AlphaFold as a pdb file (https://alphafold.com/entry/O75376) and loaded it into Pymol (2.3.0). There is quite a large portion of the structure that was ...
justinian482's user avatar
3 votes
1 answer
103 views

How to visualize electron density of a specific part of the protein residue?

Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a ...
kitsune_breeze's user avatar
1 vote
0 answers
92 views

How to identify different protein domains using HHpred

I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using ...
microbeprincess's user avatar
1 vote
1 answer
662 views

How to show electrostatic interactions in Pymol on the wanted residue

I have the following Pymol visual, The green molecule is receptor and red/yellow is the ligand. In the ligand I highlighted Lysine (K) residue as yellow. What I want to do is to highlight and draw ...
littleworth's user avatar
1 vote
1 answer
647 views

Python script to simultaneously generate multiple pdbqt files for AutoDockTools?

I have a folder of pdb ligand structures that I'd like to test in some docking experiments with a certain protein using AutoDock Vina. I am not familiar with Python so I've always been using the ...
sasam's user avatar
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1 answer
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Intrinsically disordered protein

This question has also been asked on Biostars The position that I have to visualize is in the 2700 position and this position exists in two ranges in https://www.uniprot.org/uniprot/Q12802#...
dachi's user avatar
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1 answer
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Best way to dock subset of protein PDB and definition of a ligand

I have extracted residue 45 to 88 from a PDB file (2YRQ). With that I have a new smaller PDB file. Let's call it 45_88.pdb And I want to dock it to some other full protein. My question is what's the ...
neversaint's user avatar
3 votes
1 answer
677 views

Programmatically adding hydrogen and remove water to multiple PDB files

I'm trying to dock a ligand to several hundred PDB files (receptors). I thus need to prepare the those PDB files like removing water and adding hydrogen. I can do that manually using Autodock or Pymol....
littleworth's user avatar
2 votes
1 answer
394 views

How to tell if our ligand-protein docking is good from AutoDock Vina's result

I have perform a ligand-protein docking using Autodock Vina. The result of the docking looks like this: ...
littleworth's user avatar
0 votes
1 answer
41 views

Holistic enzyme activity determination with computation [closed]

I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
ronald birb's user avatar
0 votes
2 answers
62 views

What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, meaning the ...
TRakesh's user avatar
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1 vote
1 answer
2k views

Combine structures in the same session - PyMOL

I'm a student currently looking at antibody responses against a viral target protein of interest. I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
alekoj's user avatar
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1 vote
1 answer
137 views

Outputting crunchable list of HBonds from Pymol

X-posted from the Main Stack Overflow because folks here are possibly more familiar with PyMol(?) I have been trying to assess the strength of an interface I want to mutate using Pymol. What I am ...
LauraCZD's user avatar
1 vote
1 answer
555 views

What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?

I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
Linda's user avatar
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4 votes
1 answer
309 views

How did researchers derive the Ramachandran "validation" contours?

I'm a beginner to structural biology and for fun, calculated the tortional angles of some 100, 000 proteins. Here is my Ramachandran plot: When I went to look for "canonical" Ramachandran plots, I ...
batlike's user avatar
  • 141
0 votes
2 answers
132 views

What is the difference between fixed effects and random effects in the context of Linear-mixed models?

The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
Subhash C. Davar's user avatar
1 vote
1 answer
1k views

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
2 votes
2 answers
2k views

Is there a Python package to convert InChi to molecular structures?

I am looking for a python package that can convert InChi keys (e.g.SGNXVBOIDPPRJJ-UHFFFAOYSA-N) to molecular structure or SMILES strings. Can I do that with RDKit? The key comes from: https://www....
Soerendip's user avatar
  • 1,295
3 votes
2 answers
989 views

Putting labels of different sizes on one PyMOl Object

I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
A. King's user avatar
  • 41
0 votes
2 answers
161 views

What is the best way to start with Structural bioinformatics with zero prior experience? [closed]

My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to ...
iamakhilverma's user avatar
6 votes
3 answers
3k views

Why is it necessary to add hydrogen and delete water before protein-ligand docking?

What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
Zheng Keong Ng's user avatar
5 votes
0 answers
85 views

What is a sensible forcefield choice for membrane proteins when using PDB2PQR?

I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. The goal is to calculate the electrostatic charge across the surface of the protein. There are no ...
James's user avatar
  • 409
3 votes
1 answer
75 views

predict the foldability of single-stranded DNA molecules

I have a list of regions of the human genome and I want to predict if single-stranded molecules in a buffer would tend to fold and create pin structures by sequence self-complementarity. What's the ...
719016's user avatar
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