Lucas Bleicher

6 Questions 8 Answers 0 Followers

Questions related from Lucas Bleicher

How to align sequences using Interpro profiles?

I used to be a heavy user of Pfam and its hmm profiles, and even though Interpro is supposedly its successor there is still a lot of stuff available at Pfam that is not yet available on Interpro...

23 April 2024 6,275 0 View

How to filter protein sequences (from Uniprot or Interpro) using databases such as Representative Proteomes or Reference Proteomes?

When downloading protein family alignment from very large families, I usually chose the filtered options from Pfam (Representative Proteomes or Reference Proteomes) in order to have a manageable...

03 May 2023 8,450 2 View

Software to report residues interacting with DNA/RNA in a PDB file (other than Nucplot)?

I have always used PDBsum to do a quick look at Ligplot and Nucplot outputs to see which residues in a protein are interacting with a ligand or with DNA. However, I recently found out that...

11 May 2022 7,595 1 View

Who's currently maintaining sreformat? Is there a good alternative elsewhere?

I manipulate a lot of huge alignments from PFAM in the rich, but extremely heavy, stockholm format. Sreformat was my command line tool of choice to convert from .sto to other formats (usually the...

09 September 2015 7,568 3 View

Is there a standalone program for protein structure refinement?

In a course on structural bioinformatics I teach usually do a "hands-on" class where the students do structure building (using a high resolution map and Coot) so that they have a feeling about how...

27 March 2015 3,008 3 View

Does anyone know of a statistical mechanics book with similar content to that described below?

Can anybody recommend a statistical mechanics book that: 1) is suited for self-teaching in an undergrad level 2) includes solved problems 3) includes the math needed for each topic What I have...

03 June 2014 4,021 13 View