Just random thoughts
- A truly interactive molecular graphics interface for advanced molecular dynamics simulations that an expert user can use. This interface should allow the user to manipulate objects, bring in sections of a trajectory, monitor progress, do real time “time series”, and be good to look at
- A search engine where I type in a gene and protein name and get back all the known public information on that gene protein via an interface that allows me to drill down and ask follow up questions
- The Encyclopedia of Life come to life
- Multitouch interfaces to carry out molecular modeling
- Multiscale simulation software that allows one to hook up a molecular system, e.g. a drug, with a bulk system, e.g. a cell, and evaluate the effects
Technorati Tags: Molecular Dynamics, Visualization, Molecular Modeling, Search, Encyclopedia of Life
6 Comments
Ad 2.) What about Nextbio?
Ad 2.) What about Nextbio?
Can you elaborate on what questions you’d like to ask for #2?
Can you elaborate on what questions you'd like to ask for #2?
@Berci – Not quite what I had in mind. (a) I have never used NextBio, so can only speak from hearsay, (b) and more importantly, I am talking about an open, publicly available resource.
@alf – I can try, although it’s hard. Right now, if I want to search protein structures, I to the PDB, but from there, I can’t really get to all interaction information, sequence information, etc. If I started at NCBI, I get part of the picture. Then, what if I want to find out which diseases a gene or protein has been implicated in and what pathways is it found in? Can I get all homologs right there? Get fold information, domain information, etc. You have to jump through a lot of hoops. It doesn’t have to be a resource like NCBI. All I want is a search engine that is “life science” aware and allows you to personalize look and feel to get the kinds of data you might want and also lead you to alternate options, e.g. do you want to generate a 3D structure for this sequence, or do you want to BLAST it, or do you want to find all known ligrands against this protein, etc etc. It’s in my head, just difficult to articulate right now
@Berci – Not quite what I had in mind. (a) I have never used NextBio, so can only speak from hearsay, (b) and more importantly, I am talking about an open, publicly available resource.
@alf – I can try, although it's hard. Right now, if I want to search protein structures, I to the PDB, but from there, I can't really get to all interaction information, sequence information, etc. If I started at NCBI, I get part of the picture. Then, what if I want to find out which diseases a gene or protein has been implicated in and what pathways is it found in? Can I get all homologs right there? Get fold information, domain information, etc. You have to jump through a lot of hoops. It doesn't have to be a resource like NCBI. All I want is a search engine that is “life science” aware and allows you to personalize look and feel to get the kinds of data you might want and also lead you to alternate options, e.g. do you want to generate a 3D structure for this sequence, or do you want to BLAST it, or do you want to find all known ligrands against this protein, etc etc. It's in my head, just difficult to articulate right now