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Hello,
I would like to please ask if there is any way to modify the structure using an atom in the biotite? I know that the data of individual atoms can be accessed via indexing. For example, if I …
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Could we use this code against protein structure so it can design small drug like molecules against targeted structure ? If yes any details?
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We need to do some symmetry operations on the asymmetric unit. An asymmetric unit is the smallest unique set of atomic coordinates needed to describe the repeating unit of a crystal. If we have a het…
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Congratulations on Your Open Source Release!
I'm excited to see your work on "SLAM: structure-aware lysine β-hydroxybutyrylation prediction with protein language model" available as an open-source re…
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Hi
Can Martinize2 produce coarse-grained structures and topologies from the atomistic structure of **fatty acids** (e.g. Decanoic_acid, Decanol...etc)? Or it's only for **protein**?
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Dear all,
I've installed the tool (pypka) using pip3 install pypka inside a conda envs, during these step, I do not have any error, but when i running using : python3 -m pypka parm.dat, where "p…
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Hi !
Great work !
I have encountered several issues during the docking process. And I am seeking to determine whether the issue originate from the protein structure or the ESM employed, and to pinpo…
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Hi everyone,
Thank you for an amazing tool!
I am generating the 3Di structure of a protein sequence of interest to structurally annotate against Foldseek database.
Here are the codes that I am u…
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Hello.
I am trying to find a way to save the whole protein structures with all rotamers of the mutated residue which don't have clashes.
The xl.mutate function uses only the highest probability rota…
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Thank you very much for your reply. I have a question regarding the ENM command.
1.I am currently using the PDB ID: 6DS5.
2.For a single protein structure, the issue I described previously can be …