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 ...
Aalawlx's user avatar
  • 517
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 ...
Jannik M's user avatar
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 ...
Matteo Ferla's user avatar
  • 4,234
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.
Peter's user avatar
  • 2,634
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: ...
Matteo Ferla's user avatar
  • 4,234
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 ...
llrs's user avatar
  • 4,703
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 ...
Soerendip's user avatar
  • 1,295
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. ...
Yuka Takemon's user avatar
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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
jgreener's user avatar
  • 941
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__'s user avatar
  • 12.3k
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. ...
bamblebee's user avatar
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. ...
SuleymanSelim's user avatar
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 ...
Maximilian Press's user avatar
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.
LauraCZD's user avatar
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 ...
terdon's user avatar
  • 10.1k
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-...
Laura's user avatar
  • 909
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
plat's user avatar
  • 1,032
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 ...
Maximilian Press's user avatar

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