I have studied your article "The role of disorder in interaction networks :a structural analysis". I am trying to get a list of hub -party and date- and non-hub proteins, so I am trying to get the datasets you used; however, I cant find the datasets. And so what I am asking for is that is it possible that you guide me to get the dataset somehow?

thank you for your interest in our paper. To answer your question, we employed the datasets provided as supplemental material by Han et al.,
Bertin et al. and Batada et al. Hereafter are the reference of those papers:

• Han JDJ, et al, (2004) Nature 430, 88-93


• Bertin N. et al, (2007) PloS Biol, 5(6):e153


• Batada NN et al. (2007) PloS Biol, 5(6):e154

From Han et al., Supplementary table S1 includes date and party hub information. In our paper, this is referred as FYI 2004. From Bertin et al, we used the filtered-HC Protein-Protein Interaction dataset, provided as Supplementary table S1; called FYI 2007 in our paper.

From the Batada et al. paper, we used the High-Confidence Interaction Dataset provided as Dataset S1 in the Supplementary information . As described in our paper, hubs are then defined as ORFs with more than 10 interacting partners. Finally, to determine which hub is a party or date
hub, we computed the co-expression correlation with their partners. Party hubs have a correlation higher than 0.25 with their interacting partners.

In order to perform the correlation analysis, we employed thecompendium dataset by Huges et al. [ Cell (2000) 102:109-126 ].

Where can I get access to the data driving PubNet?

Where can I get access to the data driving PubNet?

PubNet is based exclusively on PubMed, which you access via query or bulk download from the NCBI.

can you provide an example script for the integrated system for studying residue coevolution in proteins?

Regarding the integrated system for studying residue coevolution in proteins, can you provide an example script that can take one input file in command-line and write result to an output file? Also, can you send me those matlab code for SCA implementation?


The system was implemented in Java. It requires the Java virtual machine, plus some additional packages in order to run locally. If you are interested in installing it on your own machine, I can help sort out the steps. The Matlab code for SCA is unfortunately licensed and we cannot redistribute it. You may contact Rama Ranganathan for it. I think they are also releasing a newer version of SCA.

What is the Protein in the Logo at the Top of the Molmovdb Page?

I've been using your molecular movement database to find candidate proteins for a functionalization experiment that my group at Oregon State University is working on. The logo at the very top of the browsing page caught my attention (http://www.molmovdb.org/images/ProtMotDB.lrg-logo.gif). Would you happen to know what protein this is?

Lactoferrin. It's also part of Figure 4 in the original database publication from a very long time ago:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9722650

This has references to the specific structure publications.

Where is the Source Code for the Dysregulated Pathways cited in "Integrative microarray analysis of pathways dysregulated in metastatic prostate..."?

I came across your paper, "Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostrate Cancer". I am having trouble finding an appropriate algorithm to find dysregulated pathways from large clinical expression arrays and was impressed with the method you implemented. I was wondering if you happened to have the source code you used to implement IMAP and if it was possible for me to take a look at it. If so, that would be of enormous assistance to me.

Unfortunately there is no code floating around to perform the analyses you want to do. I did the calculations for the paper you cited but I did them three years ago and the computations were done mostly interactively in an R terminal.

How does one get the corresponding frequencies for the normal modes for which you have generated the movies?

Regarding http://molmovdb.org/nma/, how does one get the corresponding frequencies for the normal modes for which you have generated the movies?

No normal modes are extracted in the process of making the movies

What are the datasetsfor Hinge Atlas and Hinge Gold?

I found the database of your lab is very useful at http://www.molmovdb.org/cgi-bin/browse.cgi, which include many data sets of conformations. My current program can read the pdb files.

Could you send me with the database?




You might find the Hinge Atlas and Hinge Atlas Gold datasets the best curated and easiest to download. You can find the download links and instructions at: http://molmovdb.org/cgi-bin/sets.cgi.

Please cite our Hinge Atlas and/or FlexOracle papers if you use these datasets:

http://papers.gersteinlab.org/e-print/HingeAtlas/preprint.pdf
http://papers.gersteinlab.org/e-print/flexoracle/preprint.pdf