PDBaser
Protein preparation for MD, made faster and easier ! (by mimminou)
biomisc
collection of miscellaneous command line bioinformatic scripts (by olgatsiouri1996)
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| PDBaser | biomisc | |
|---|---|---|
| 1 | 2 | |
| 14 | 7 | |
| - | - | |
| 3.6 | 4.5 | |
| 4 months ago | 5 months ago | |
| Python | Python | |
| GNU General Public License v2.0 only | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
PDBaser
Posts with mentions or reviews of PDBaser.
We have used some of these posts to build our list of alternatives
and similar projects.
-
PDBaser, an open source protein preparation tool.
Link : https://github.com/mimminou/PDBASER
biomisc
Posts with mentions or reviews of biomisc.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-06.
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Biopython quarry on protein sequencing
if you know witch exactly residues do you want to retrieve from your pdb you can use this: subset_pdb_to_fasta.py
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Extract sequences given FASTA + list of starts and ends?
i have made one with python: trim_fasta_by_coords.py. I have a newer version that deals with strands but since you work with proteins you don't need it
What are some alternatives?
When comparing PDBaser and biomisc you can also consider the following projects:
pdbr - pdb + Rich library
DnaChisel - :pencil2: A versatile DNA sequence optimizer
tm_calculator_gui - Calculates the melting temperature(in Celsius) of a user imported forward and reverse primer based on primer blast default parameters & pcr additives
pyfaidx - Efficient pythonic random access to fasta subsequences
pycm - Multi-class confusion matrix library in Python
readfq - Fast multi-line FASTA/Q reader in several programming languages