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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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 ...
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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...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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#...
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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 ...
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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....
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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:
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ?
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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 ...
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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....
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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 ...
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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 ...
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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.
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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 ...
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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 ...
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