User: rayoub

gravatar for rayoub
rayoub100
Reputation:
100
Status:
Trusted
Location:
Last seen:
9 hours ago
Joined:
2 years, 3 months ago
Email:
r**********@outlook.com

Posts by rayoub

<prev • 21 results • page 1 of 3 • next >
0
votes
0
answers
124
views
0
answers
Comment: C: Will de novo protein structure prediction research become irrelevant?
... I agree that is exciting research. On the other hand, I'm wondering if homology modelling is becoming increasingly sufficient since for most sequences there will be known homologous structures. That is, as structural genomics proceeds there will be fewer and fewer cases of de novo modelling being ne ...
written 2 days ago by rayoub100
0
votes
0
answers
124
views
0
answers
Forum: Will de novo protein structure prediction research become irrelevant?
... Will de novo protein structure prediction research become irrelevant as structural genomics advances and the number of solved structures available for homology modeling increases? I also asked this question on research gate but answers there often come at a glacial pace. ...
forum protein structure prediction written 2 days ago by rayoub100 • updated 2 days ago by genomax59k
0
votes
1
answer
155
views
1
answers
Comment: C: Neural networks feature importance
... I agree. But in this case he said 'binary classification'. ...
written 8 weeks ago by rayoub100
0
votes
1
answer
155
views
1
answers
Comment: C: Neural networks feature importance
... I could be wrong but I sense a misunderstanding here. A neural network for binary classification typically learns an output distribution, not a function. So their should only be one output, probability of a positive output given the inputs. 1 minus this value would then be the probability of a negat ...
written 8 weeks ago by rayoub100
1
vote
0
answers
121
views
0
answers
What is the fastest protein structure alignment?
... As the title suggest, I would like to know what is the fastest pairwise protein structure alignment tool available that still manages to be accurate. The best I know of currently is CE. ...
protein structure structure alignment written 9 weeks ago by rayoub100
2
votes
2
answers
165
views
2
answers
Answer: A: Pfam search uses seed or full alignments?
... I was once confused by this. It seems definitions are not as clear in bioinformatics as they are in mathematics and misunderstanding is common. If you click on the 'download' link once you follow your link above you will see the NSEQ field which has the value 207. This seed alignment defines the fam ...
written 12 weeks ago by rayoub100
3
votes
1
answer
832
views
1
answers
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 9 months ago by rayoub100
5
votes
1
answer
406
views
1
answer
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 9 months ago by rayoub100 • updated 9 months ago by Bill Pearson830
3
votes
1
answer
764
views
1
answer
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 20 months ago by rayoub100 • updated 18 months ago by wojdyr40
2
votes
1
answer
421
views
1
answer
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 22 months ago by rayoub100 • updated 21 months ago by Petr Ponomarenko2.5k

Latest awards to rayoub

Supporter 9 weeks ago, voted at least 25 times.
Scholar 12 weeks ago, created an answer that has been accepted. For A: Biopython pairwise2 alignment: is one_alignment the best alignment?
Scholar 9 months ago, created an answer that has been accepted. For A: Biopython pairwise2 alignment: is one_alignment the best alignment?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Biopython pairwise2 alignment: is one_alignment the best alignment?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 977 users visited in the last hour