 |
|
| FriendFeed is the easiest way to share online. Learn more » |
Warren DeLano - http://bytesizebio.net/index...
lazyweb: what is the best (free) set up to try out ligand docking in large scale. Any recent good reviews on the methods ?
Michael Kuhn, Steve Koch and Jean-Claude Bradley liked this
I am going to try autodock. Anyone here on friendfeed has a better suggestion ?
- Pedro Beltrao
Autodock would be my recommendation as well unless there is something new out there that I haven't tracked.
- Deepak Singh
Autodock seems to be widely-used and well-regarded. Could also try zdock - more lightweight and good for command-line scripting, parsing.
- Neil Saunders
zdock is more protein-protein centric. Did they add small molecule stuff?
- Deepak Singh
from IM
Ah, that's true. Haven't used it in a while. Autodock would be better for ligands.
- Neil Saunders
wondering how difficult it would be to integrate #autodock into #bioclipse or with the #cdk ...
- Egon Willighagen
can Autodock actually be scripted from the command line? Or am I restricted to using their GUI to create input files?
- Egon Willighagen
I believe they had developed a python based framework
- Deepak Singh
from IM
they have command line tools but I am still wrapping my head around the basics
- Pedro Beltrao
FRED (not Open Source) is very easy to use, but maybe not as accurate as others. If accuracy is the goal it seems that Glide does a good job.
- Rajarshi Guha
Glide is definitely state of the art. The one thing about docking though is no one tool is good enough. Pretty much every company I know that does a lot of virtual screening uses two tools
- Deepak Singh
from IM
Thanks for the suggestions. Does anyone know if Glide free for academics ?
- Pedro Beltrao
Experimental evolution of bet hedging - http://www.citeulike.org/user...
Combinatorial binding predicts spatio-temporal cis-regulatory activity - http://www.citeulike.org/user...
listening to the new Pearl Jam album http://tinyurl.com/ly2u27,not too bad but I would gladly take suggestions for new bands to explore :)
My Most Expensive Paper - http://omicsomics.blogspot.com/2009...
Edgetic perturbation models of human inherited disorders - http://www.citeulike.org/user...
from the people that brought you "party" and "date" hubs .. we have now "edgetic"
- Pedro Beltrao
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator - http://www.citeulike.org/user...
Neil Saunders liked this
PepX: a structural database of non-redundant protein-peptide complexes. - http://www.ncbi.nlm.nih.gov/entrez...
Neil Saunders liked this
Analysis: Limited agreement among lists of Cdc28p substrates - http://larsjuhljensen.wordpress.com/2009...
DRYGIN: a database of quantitative genetic interaction networks in yeast. - http://www.ncbi.nlm.nih.gov/entrez...
Pawel Szczesny and Ruchira S. Datta liked this
umm .. everything is password protected. Not a very useful database if you cant actually use it.
- Pedro Beltrao
they might have been aiming for January 2010, when the NAR db issue officially comes out
- Michael Kuhn
It makes sense, since the data they have on this database is part of paper that Boone talked about and that I assume is currently under review. Still .. annoying :)
- Pedro Beltrao
yep, I just got the email response back. They will remove the password protection when the other paper describing the data is published. Bummer :)
- Pedro Beltrao
Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans - http://www.citeulike.org/user...
No mention to friendfeed: RT @BoraZ Should You Be Tweeting? (as a scientist) by Laura Bonetta: http://www.cell.com/fulltex... in Cell
Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling - http://www.citeulike.org/user...
Comparing cellular proteomes by mass spectrometry - http://genomebiology.com/2009...
'Edgetic' perturbation of a C. elegans BCL2 ortholog - http://www.citeulike.org/user...
Ruchira S. Datta and Neil Saunders liked this
Not sure if I like the (made-up) word 'edgetic' though ;-)
- Neil Saunders
Vidal lab is buzzword heavy :)
- Pedro Beltrao
Mislocalized Activation of Oncogenic RTKs Switches Downstream Signaling Outcomes - http://www.citeulike.org/user...
R 2.10.0 is Out! - http://onertipaday.blogspot.com/2009...
Google's social search is very cool. An easy way to search for that content I remember reading but not sure where.
Survey of large protein complexes in D. vulgaris reveals great structural diversity - http://www.citeulike.org/user...
Goodbye from Nature Reports Stem Cells - http://blogs.nature.com/nautilu...
Evolution of biomolecular networks |[mdash]| lessons from metabolic and protein interactions - http://www.citeulike.org/user...
After almost 3h I am finally on my home again. A lot of time to figure out that toilet paper is not a bomb. #caltrain
Bummer.
- Chris Lasher
Caltrain hell tonight, got more news of the delays from twitter than from caltrain people
Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins - http://www.citeulike.org/user...
Other ways to read this feed:
