8
votes
Accepted
Machine learning using protein-sequences
There are two types of features which can be extracted from protein sequences. It is not possible to known which, if any, of these features would be useful in classification tasks. It may not be ...
- 527
6
votes
Accepted
Why do we need to find minimum energy in a protein chain?
After translation, proteins fold to achieve a specific 3D structure which allows them to perform their specific functions. The structure of a protein computationally inferred through energy ...
- 106
3
votes
Why is there a chloride ion in this 3D model?
It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a ...
- 4,274
3
votes
Accepted
Receptor-ligand database
CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions.
The interactions can be searched or downloaded.
- 2,644
2
votes
How to calculate Gene Ontology terms in python
You can calculate gene ontology similarity with the GOSemSim R package (paper)(disclaimer I'm a contributor to this package). You have several similarity scores implemented, some of them are across ...
- 4,721
2
votes
Post docking evaluation
You can run a Molecular Dynamics simulation to see if the pose is stable and whether the protein changes/adapts it’s conformation.
You can calculate the ligand efficiency, the docking score divided ...
- 1,305
2
votes
Receptor-ligand database
Have you tried STRING?
It's a publicly available protein-protein interaction database, so it won't be a complete picture.
Ingenuity Pathways Analysis (IPA) is really nice but is a paid service. ...
- 121
2
votes
Accepted
How to calculate lipophilicity of proteins?
Oligopeptide
The lipophilicity of an oligopeptide or a small molecule can be calculated with RDKit, the classic compChem python toolkit. The measure is logP or partition coefficient, namely the ...
- 4,274
2
votes
What is the best way to start with Structural bioinformatics with zero prior experience?
As others have said, there is no short cut and you will need to spend some time with a good book.
I would say there are 3 broad areas of understanding you have to have as a structural ...
- 951
2
votes
Cytoscape for coloring the nodes in the network
Answering this (2 years later) in case others stumble upon it.
Yes! You can certainly color your proteins by category. This is a very common use of Cytoscape. I'd recommend the data visualization ...
- 151
2
votes
PyMol: Output Polar Contacts Between Chains to Text File
So you can install PyMOL as a standalone, but you can also install it as a bona fide Python 3 module via conda:
...
- 4,274
1
vote
ProteinPromt installation
The docker file is here https://codebase.helmholtz.cloud/proteinprompt/ProteinPrompt/-/blob/main/Dockerfile
You need to download and install a copy of Docker (below).
These are the instructions how to ...
M__♦
- 13k
1
vote
How can I extract the Protein distance map data in Julia?
for someone who have same question as mine...
this helps you to extract distance map data file.
...
- 21
1
vote
How can I clean a PDB file using VMD or NAMD?
You can use Chimera for this. The following code cleans your pdb file and write new pdb file.
...
- 118
1
vote
Accepted
What's the difference between Barycenter Centrality and Closeness Centrality (Freeman)?
First, I'll observe that Freeman centrality as you define it is the reciprocal of the Barycenter centrality as you define. It looks like people often use the reciprocal instead of the original ...
- 4,262
1
vote
Outputting crunchable list of HBonds from Pymol
Thanks a lot to all who commented/replied, the author of the scripts provided a response. It was down to a syntax change in PyMol of which I wasn't aware that caused my selection to come up empty.
- 21
1
vote
Accepted
Difference between PPI networks and Gene Co-expression networks
Based on my rudimentary understanding, PPIs are constructed from gene co-expression networks
Not really, no. PPI stands for protein-protein interaction. In PPI networks, each node is a protein and ...
- 10.6k
1
vote
Can I automate CLUSTALO and output alignment sequence identity?
So, as the first reply said, there's sort of multiple questions here.
For filtering things out from a table, I would absolutely use pandas. https://swcarpentry.github.io/python-novice-gapminder/08-...
- 1,027
1
vote
What is the best way to start with Structural bioinformatics with zero prior experience?
A good starting point could be this book by Gu and Bourne:
Structural Bioinformatics, 2nd Edition
- 1,062
1
vote
pvalue calculation of protein-protein network with permutation test
It is probably necessary to correct for the degree distribution of the network, I am not sure that a tool such as the Mantel test will quite do this (as suggested by user Michael G.). In naturally ...
- 4,262
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