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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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 ...
1 vote
0 answers
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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 ...
0 votes
2 answers
193 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 ...
3 votes
1 answer
56 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 ...
1 vote
0 answers
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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 ...
1 vote
1 answer
232 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 ...
1 vote
1 answer
250 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 ...
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1 answer
35 views

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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1 vote
1 answer
42 views

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 ...
3 votes
1 answer
388 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....
2 votes
1 answer
192 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: ...
0 votes
1 answer
37 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 ...
0 votes
2 answers
52 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 ...
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1 vote
1 answer
719 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 ...
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1 vote
1 answer
104 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 ...
1 vote
1 answer
223 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 ...
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4 votes
1 answer
217 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 ...
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2 answers
107 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 ?
1 vote
1 answer
890 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 ...
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....
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3 votes
2 answers
703 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 ...
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0 votes
2 answers
128 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 ...
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5 votes
3 answers
1k 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.
5 votes
0 answers
69 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 ...
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3 votes
1 answer
67 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 ...
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