Tuesday, May 29, 2007

Packing Software on Mac OS X

The packing software on molvovdb geometry site working on Mac OS X? If not, can you help with porting it to work on Mac OS X?

There has been problems compiling the program and making it work on Mac OS X. The program was written by a lab member who no longer is available for this. Please continue using the web interface.

PNAS Paper Error

Regarding the PNAS paper titled Genomic analysis of the hierarchical structure of regulatory networks, I am having trouble understanding the organization of the columns. How was the placement of proteins in columns determined? And what is the purpose behind the duplication of level 1 proteins such as SPT8, and gaps within the columns?

Unfortunately, I think that is a typo when PNAS edited our paper. It is not in our pdf file that we sent to PNAS.

Sunday, May 20, 2007

Background Probability

In your paper, "Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures" what is the background probability for the Viterbi and forward algorithm you used?

We used spatial ellipsoid of coordinate dist. in ali. for atom's position and used a flat prior in estimating this.

Table 1 Discrepancy

Regarding the Science paper titled Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights the numbers in the Table 1 tell something different. According to Table 1, Simultaneously possible interactions have less fraction of same functions, as well as less fraction in co-expression correlation. Can you please clarify?

The table headings unfortunately got switched at some unknown point during copy editing. We have posted a note to that point on our site. Do let me know if you need more help on this!

Friday, May 18, 2007

Sieve-Fit Program

Regarding the availability of the "sieve-fit". Do you have the program (source, script or whatever) or know who could provide it to me?

see http://geometry.molmovdb.org/


Unix Version of Voronoi Calculator?

Where is there a stand alone version of the Voronoi packing efficiency calculator program for unix platform?
The website runs the packing-eff.exe program (in src-prog3/ folder)from this package:


Currently there is no unix version.

Monday, May 14, 2007

How do I get your original, published papers online?

How do I get your original, published papers online?

Essentially all of my work is available on-line. Go to:


and click on the appropriate "preprint" link. You will be get a preprint or (if appropriate) journal reprint of the paper you want. There should be NO password challenges or other barriers. Usually, the papers are in PDF format but some are in HTML. (Other formats are available directly from http://papers.gersteinlab.org/e-print.)

Please let me know if you have any problems with this service. If you can't get
what you want, we can easily post you normal paper reprints.

PS I'm CC'ing this message to our FAQ archive (faq@bioinfo.mbb.yale.edu) as it
enables me to track the popularity of various papers.