Yasser Almeida Hernandez

8 Questions 8 Answers 0 Followers

Questions related from Yasser Almeida Hernandez

How can you improve primer design for archaea gene cloning?

I am designing primers to clone membrane protein homologs from several archaea organisms in E. coli. The templates sequences are very CG enriched, resulting in high Tm temperatures, %CG and...

12 December 2014 7,274 2 View

N- and C-terminal residues?

Which amino acids are the most frequent in the N- and C-terminal positions? Is there some work about this issue?

01 January 2014 6,085 1 View

Which value of timestep would be better for a 40 ns MD simulation with NAMD?

I am working with a 153 aa protein.

12 December 2013 9,131 6 View

NAMD vs GROMACS?

I am working with a 153 aa protein to evaluate the influence of point mutations in the stability and folding, by molecular dynamics simulations. To this task, which package would you recommend,...

12 December 2013 3,848 0 View

What Kd cut-off values are the accepted for consider a protein-ligand complex with a low, medium or high affinity?

Kd cut-off values

12 December 2013 5,701 6 View

Tools to analyze protein-protein interactions (PPI)?

I have a list a several proteins and I want to search for interactions between them directly by a second or third protein. Which are the more suitable tools to do this? I've used Cytoscape for...

09 September 2013 1,583 5 View

How to get ontologies from a PDB IDs list?

I have a list of PDB IDs list and I need to get ontology data to verify any enrichment of protein family, function, cellular localization, etc. Which tool is the more suitable?

12 December 2012 9,090 1 View

Lysosomal vs. Nuclear EGFR Trafficking

Upon Ligand binding (EGF, TGF-alpha) EGFR is internalized and finally sorted to degradation in lysosomes, or translocated to the nucleus, where it regulates the expression of several genes. Which...

06 June 2012 9,558 4 View