Tagged Questions
0
votes
0answers
27 views
Modeller - Convert FASTA to PIR
I am doing a basic modelling following the instructions here. But different target / template sequences.
http://salilab.org/modeller/tutorial/basic.html
Do I need to convert the FASTA to PIR with a ...
4
votes
1answer
97 views
How does MEME compute the background frequency of nucleotides?
I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.
I would like to know how MEME estimates the background ...
3
votes
1answer
46 views
How do I view the simulated protein structure along with ligand in VMD?
I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
2
votes
0answers
60 views
Software for counting fly eggs
Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
2
votes
3answers
45 views
What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
4
votes
2answers
83 views
Biological key file format
I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data.
Thanks
9
votes
1answer
138 views
Is there a program that simulates biology on a molecular level?
Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
3
votes
2answers
117 views
JMol “calculate HBONDS”: which atom is the donor/acceptor?
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds.
Here's one line from an example ...
4
votes
1answer
49 views
Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology
Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?
I have tried the following:
...
