User: rayoub

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rayoub80
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Posts by rayoub

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Answer: A: Biopython pairwise2 alignment: is one_alignment the best alignment?
... There may be multiple pairwise alignments that have the same optimal score with respect to gap penalty and match scoring. The function just returns the first it finds during the traceback of the dynamic programming matrix rather than returning all of them. From the following link, several paragrap ...
written 3 months ago by rayoub80
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Pfam alignments: full vs uniprot
... I'm a bit confused by the alignment page of a Pfam entry. They provide the 'seed' alignment from which the initial HMM is created. They also provide the 'full' alignment that, to my understanding, is created by searching the UniProtKB and adding in those proteins significantly similar to the seed HM ...
alignment pfam written 3 months ago by rayoub80 • updated 3 months ago by Bill Pearson820
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Tool: RUPEE: Fast Protein Structure Search
... As a computer science PhD student, I have developed a fast protein structure search called RUPEE. It searches among the 309,000 CATH domain structures as of CATH v4.1. It is notable for being extremely fast in comparison to existing protein structure searches while maintaining a good level of precis ...
protein structure tool written 4 months ago by rayoub80
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PDB missing residues vs inserts
... I think I missed a detail in my understanding of missing residues. I understand that in some cases residues don't end up as part of the PDB model because of crystallization issues. However, aside from that case, will numbers be missing in the sequence of residues even though the residues are contigu ...
pdb written 14 months ago by rayoub80 • updated 12 months ago by wojdyr40
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resno fields within a pdb file
... Are the resno fields within the ATOM records of PDB files within a single chain always consecutive? I understand insertion codes may be present. Aside from that, are they always consecutive regardless of what index they start at? ...
pdb protein structure protein written 16 months ago by rayoub80 • updated 16 months ago by Petr Ponomarenko2.5k
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Comment: C: isoforms and the definition of a protein
... This is a fantastic explanation. Your last sentence is what it boils down to. I have to figure out what I want and normalize the data per application. I want to play around with predicting residue-residue contacts from sequence alone within a single protein chain but what it looks like I have to d ...
written 16 months ago by rayoub80
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isoforms and the definition of a protein
... I'm reviewing the UniProt data model and I'm confused by what is a protein. Originally, I thought that a protein was defined by its sequence of amino acids. However, the fact that isoforms of a gene are stored in one entry for UniProt/Swiss-Prot leads me to believe a protein is defined by the gene f ...
protein isoforms proteins written 16 months ago by rayoub80 • updated 16 months ago by cdsouthan1.8k
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Comment: C: Retrieve all distinct domains from PDB (or lots of them)?
... Rather than clarify my question I'm going to look at the ICM-Browser and do as you instruct below. If that is not free I'll try it with PyMOL. Haven't used either yet. I think you are right in that I've gone as far as I could with juggling the concepts in the abstracts and I need to put my head back ...
written 16 months ago by rayoub80
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Comment: C: Retrieve all distinct domains from PDB (or lots of them)?
... Head exploding now. Your answer is very informative and the exploding is not due to misunderstanding but understanding it is more complicated than initially thought for a CS/MATH person to address in a vacuum. When CASP puts out a structure target for folks to try to predict because it will be soon ...
written 16 months ago by rayoub80
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Comment: C: Retrieve all distinct domains from PDB (or lots of them)?
... That is very interesting. Then from what I can tell, if one were to mine PDB structures to predict contact or conformations then the best level to do this at is the level of the chain since domains within chains will have different conformations depending on the chain (sequence) they are taking part ...
written 16 months ago by rayoub80

Latest awards to rayoub

Scholar 3 months ago, created an answer that has been accepted. For A: Biopython pairwise2 alignment: is one_alignment the best alignment?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Biopython pairwise2 alignment: is one_alignment the best alignment?

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