Questions tagged [structural-biology]
Questions relating to the structure (3-D conformation) of biological molecules, such as protein, RNA and DNA.
9
questions
3
votes
1answer
38 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 ...
0
votes
3answers
65 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
1answer
29 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 ...
1
vote
2answers
25 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....
3
votes
2answers
146 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 ...
0
votes
2answers
60 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 ...
3
votes
3answers
117 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.
2
votes
0answers
21 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. There are no lipids in the structure.
PDB2PQR has predefined options of amber, charmm, parse, tyl06, ...
3
votes
1answer
56 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 ...
