Yasser Almeida Hernandez

7 Questions 6 Answers 0 Followers

Questions related from Yasser Almeida Hernandez

Trajectory with transformed coordinates?

Hello, I have two different simulations of a membrane protein in a E. coli model membrane, and I want to analyze the protein-lipids interactions, by generating 2D density maps. In each...

27 August 2018 7,790 3 View

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...

17 December 2014 9,061 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?

17 January 2014 1,373 1 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

11 December 2013 5,791 8 View

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

I am working with a 153 aa protein.

03 December 2013 2,606 5 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...

06 September 2013 3,723 4 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?

20 December 2012 110 1 View