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Is it not possible to use mk_prepare_receptor to prepare a pdb file for flexible docking only and not for reactive docking?
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OpenMM's topology objects and readers/writers don't provide enough chemical information to actually parameterize small molecules nonstandard biopolymers, post-translational modifications, glycosylatio…
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Hackathon idea, as discussed in the UGM talks:
- move the mmCIF parser from the e-PDB folks into the core RDKit codebase.
See also #1584
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Hello! What a wonderful program you have here.
I was writing to ask if lightmotif is capable of searching for motifs in protein sequences. It looks like functionality is partially in place but I c…
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Hi,
I (and my code) were a bit surprised by entry 3mgn__C1_UNDEFINED--3mgn__L1_UNDEFINED where the ligand seems to be a D-peptide - is it intended that this kind of protein be included in the datas…
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pombe fxn1 is picking up a mapping to cellular iron ion homeostasis KW-0409
I think to the best of current knowledge this protein is involved in iron-sulfur cluster assembly, it doesn't regulate th…
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Hi @edwintse @TomkUCL @lindapatio @jemimahaque
We need more about the project on the wiki - describing the story so far.
https://github.com/StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B/…
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Thanks for an excellent package.
My issue is as above. Certain amino acid sequences simply crash with an error of type
`[1] 132848 segmentation fault (core dumped) ./derna -i ~/test.fasta -o o…
h-ahl updated
1 month ago
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The alignments are defined in such a way that it is not possible to have consecutive gaps. Here's a test case (to go in NeedlemanWunschTest. Requires 4bc1d20.):
``` java
@Test
public void testSin…
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Heya :) So I'm running version 112. I go through a few steps with the data so apologies for the long question :)
The original data is:
``#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT case.bam
c…