FAQ

From GersteinInfo

OLD FAQs

Frequently asked questions about lab programs (mailman version, blogger version)

NEW FAQ

Browse new FAQ here http://groups.google.com/group/gerstein-lab-faqs?hl=en

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!

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.

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.

Packing

 On 4/8/10 2:22 AM... wrote:
 >                        We  would like to calculate the  packing density
 > within proteins. From your website we found an option to calculate the
 > Voronoi volume of protein atoms. For packing density the volume enclosed
 > within the van der Waal's envelope of the  protein atoms also needs to
 > be calculated. Could you could guide us to such a program available in the
 > public domain which does the above.
 >                                                   with warm regards,

Best to use the "packing-eff" program. (See http://geometry.molmovdb.org/files/libproteingeometry/src-prog3 )