User: jgreener

gravatar for jgreener
jgreener70
Reputation:
70
Status:
Trusted
Location:
United Kingdom
Website:
http://jgreener64.gith...
Last seen:
3 days, 3 hours ago
Joined:
4 years, 3 months ago
Email:
j*******@hotmail.co.uk

Posts by jgreener

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
73
views
1
answers
Answer: A: Help regarding protein modelling and docking. Can anybody provide me a protocol/
... I think by fragment you mean sequence - fragment usually has a different meaning, referring to a short structural motif (e.g. the structure of 5 amino acids from a larger structure). If the protein has available templates then I-TASSER, SWISS-MODEL, PHYRE2 and others will all give you decent models ...
written 3 days ago by jgreener70
3
votes
1
answer
123
views
1
answers
Answer: A: Evaluating protein structure predictions
... Your sequences are ~50 residues, which is fine for protein structure prediction. The minimum length limit is a grey area and depends on things like available templates, secondary structure v. disorder propensity and availability of sequences to get coevolution constraints. But for sure you can do me ...
written 21 days ago by jgreener70
0
votes
2
answers
261
views
2
answers
Comment: C: What is the best/mostcommon approach to model the effect of missense SNP on prot
... Sorry, I am not the developer, it was made in my PhD lab but after I left. I don't have enough knowledge of the tool to write a Tool post. ...
written 26 days ago by jgreener70
1
vote
2
answers
670
views
2
answers
Answer: A: what is the threshold RMSD value for determining protein structure similarity
... To add to the above answer, RMSD is dependent on the size of the protein. If you are looking for a cut-off score, with all the caveats that entails, I would recommend using [TM-score][1] (or the related [TM-align][2]). TM-score runs from 0 to 1 and a TM-score of 0.5 or higher indicates that the two ...
written 27 days ago by jgreener70
1
vote
2
answers
261
views
2
answers
Answer: A: What is the best/mostcommon approach to model the effect of missense SNP on prot
... The recently-released [Missense3D][1] provides a nice interface to explore this problem. [1]: http://www.sbg.bio.ic.ac.uk/~missense3d/index.html ...
written 27 days ago by jgreener70
0
votes
1
answer
105
views
1
answers
Answer: A: Where can I get promotif?
... As an alternative, [DSSP][1] may have some of what you need. [1]: http://swift.cmbi.ru.nl/gv/dssp/ ...
written 27 days ago by jgreener70
1
vote
1
answer
95
views
1
answers
Answer: A: Grouping protein domains into categories?
... There are a few resources for organising protein domains: - [CATH][1] sorts domains by structure into class, architecture, topology and homologous superfamily. - [ECOD][2] sorts domains by evolutionary relationship into architecture, possible homology, homology, topology and family level. - [SCO ...
written 27 days ago by jgreener70
1
vote
2
answers
119
views
2
answers
Answer: A: Protein structure to classify domain sequences into full Vs. partial lengths and
... I'm not completely clear what you are trying to do, but I would consider using the alignment with sequences or HMMs to check the domain boundaries rather than using structure prediction. This will be more sensitive than secondary structure prediction, which uses local sequence features and is less a ...
written 27 days ago by jgreener70

Latest awards to jgreener

Scholar 21 days ago, created an answer that has been accepted. For A: Evaluating protein structure predictions
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Evaluating protein structure predictions

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2085 users visited in the last hour