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KarrLab
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bpforms
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
https://www.bpforms.org
MIT License
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refactor order of operations of protonation
#60
jonrkarr
closed
5 years ago
1
extract N,C protein positions
#59
jonrkarr
closed
5 years ago
1
Add sequence feature
#58
jonrkarr
closed
5 years ago
1
Add validation of subunits and dimers
#57
jonrkarr
closed
5 years ago
1
Set upper sequence length limit on website and warning message
#56
jonrkarr
closed
5 years ago
1
Add OpenBabel image and dimers to HTML visualizations of alphabets
#55
jonrkarr
closed
5 years ago
1
Calculate circular structures
#54
jonrkarr
closed
5 years ago
1
Add circular to cli, REST, web form
#53
jonrkarr
closed
5 years ago
1
Add methods to calculate structure of BpForm and export structure to InChI format
#52
jonrkarr
closed
5 years ago
1
add test for example jupyter notebook
#51
jonrkarr
closed
5 years ago
1
Replace "amino acid" terminology with "protein residue" for consistency with RESID
#50
jonrkarr
closed
5 years ago
1
Encapsulate representation of backbones, bonds
#49
jonrkarr
closed
5 years ago
1
Add docs section for future directions
#48
jonrkarr
closed
5 years ago
1
Describe how to contribute to alphabets in the docs
#47
jonrkarr
closed
5 years ago
1
Switch rest to post queries
#46
jonrkarr
closed
5 years ago
1
bpforms as command line: problem with validate and user-defined expression
#45
ychebaro
closed
5 years ago
1
Allow spaces in structure
#44
jonrkarr
closed
5 years ago
1
Write cover letter
#43
jonrkarr
closed
5 years ago
1
Consider limiting DNA alphabet to verified entries
#42
jonrkarr
closed
5 years ago
1
Protonate alphabets to pH 7.4, calculate major tautomer
#41
jonrkarr
closed
5 years ago
1
Add error logging to web server
#40
jonrkarr
closed
5 years ago
0
Refine alphabets
#39
jonrkarr
closed
5 years ago
0
Reach out to potential users
#38
jonrkarr
closed
5 years ago
4
Add attribute for originating monomer
#37
jonrkarr
closed
5 years ago
1
Set backbones for alphabets consistent with DNAmod, MODOMICS, RESID
#36
jonrkarr
closed
5 years ago
1
Rename alphabets
#35
jonrkarr
closed
5 years ago
1
Display images of monomer in website
#34
jonrkarr
closed
5 years ago
1
Rename Base --> Monomer
#33
jonrkarr
closed
5 years ago
1
Add backbone formula, charge
#32
jonrkarr
closed
5 years ago
1
Upgrade server
#31
jonrkarr
closed
5 years ago
1
Fix alphabet table width
#30
jonrkarr
closed
5 years ago
1
Get docs searching working
#29
jonrkarr
closed
5 years ago
1
Proofread
#28
paulflang
closed
5 years ago
0
Add Jupyter notebook with example
#27
jonrkarr
closed
5 years ago
0
Allow spaces and parentheses in base characters for DNAmod alphabet
#26
jonrkarr
closed
5 years ago
1
Move grammar to text file and include file in docs
#25
jonrkarr
closed
5 years ago
1
Look for better REST API package
#24
jonrkarr
closed
5 years ago
1
Speedup protonation via using java library
#23
jonrkarr
closed
5 years ago
1
Speedup protonation via batches
#22
jonrkarr
closed
5 years ago
1
Allow unicode characters in alphabet
#21
jonrkarr
closed
5 years ago
1
Link to sandbox from website, docs, README
#20
jonrkarr
closed
5 years ago
1
Cleanup or delete test code for DNAmod
#19
jonrkarr
closed
5 years ago
1
Proofread website, documentation
#18
jonrkarr
closed
5 years ago
2
Use ChemAxom Marvin for better protonation
#17
jonrkarr
closed
5 years ago
1
Update release for publication submission
#16
jonrkarr
opened
5 years ago
0
Add example to sandbox
#15
jonrkarr
closed
5 years ago
1
Id, name, description for alphabets
#14
jonrkarr
closed
5 years ago
1
REST API for alphabets
#13
jonrkarr
closed
5 years ago
1
Change chars rule to end in capital letter
#12
jonrkarr
closed
5 years ago
1
Build protein alphabet from RESID
#11
jonrkarr
closed
5 years ago
1
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