User: michael

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michael0
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Posts by michael

<prev • 5 results • page 1 of 1 • next >
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Editing angles of PDB files
... I'm trying to create a protein folding simulation where I have a pdb file with six amino acids that I know make up an alpha helix. My goal is to change the backbone angles such that it no longer represents an alpha helix and then have the algorithm find the correct conformation again. I was hoping ...
pdb python structural-biology written 6 months ago by michael0 • updated 6 months ago by Biostar ♦♦ 20
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Protein-Protein interaction modelling without 3D structure
... Hi, I am currently looking into four proteins that are supposed to interact with each other. I would like to find out what exact residues are responsible for the interaction, the only problem is that I don't have a structure for any of them. All of the algorithms I've found require a known structur ...
protein-protein-interaction modelling written 16 months ago by michael0 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: Strategies for identifying as many homologs as possible
... Hi Michael, thanks so much for your detailed answer! I agree that I do not need to be too worried about missing a few orthologs here and there. That being said, I would like to have a table stating how many species within different subgroups have a copy of this gene (e.g. 28 Fungi have a homolog). ...
written 22 months ago by michael0
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Strategies for identifying as many homologs as possible
... I am working on a follow-up to a study done in 2006. In it, the authors attempted to identify "all homologs" of a gene (using blastp and tblastn) and they looked at its likely evolution. (The gene is very highly conserved across species). There were a number of interesting questions that the authors ...
homology phylogenetics est msa blast written 22 months ago by michael0 • updated 22 months ago by Michael Dondrup47k
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Neighbor Joining algorithm: why n-2?
... I have been looking into how the neighbor joining algorithm works and I have two questions about the first step, i.e. computing the matrix Q using the following formula: > Q(i,j) = (n - 2)d(i,j) - Σd(i,k) - Σd(j,k) Where both summations are from k = 1 to n, n is the number of taxons, d() is the ...
neighbor-joining phylogenetics evolution written 2.2 years ago by michael0 • updated 2.2 years ago by kloetzl1.1k

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