Wednesday, October 24, 2007

Mixed up figures in "Divergence of TFBS across related yeast species"

I am a PhD student at CS Dept, Univ of Washington, Seattle. From your Science paper "Divergence of TFBS across related yeast species" I have some questions.
  • Should Fig 2C be current Fig 2E?
  • Should Fig 2D_1 be current Fig 2C?
  • Should Fig 2E be current Fig 2D_1?
Looks like the Figure legend was mixed up. The text in the paper matches
up with the Figure, but in the legend parts C-E are mixed up. It should

Comparison of binding by Ste12 and Tec1 across S. cerevisiae (red), S.
mikatae (blue), and S. bayanus (green). (A) Conserved binding. (B)
Conserved binding with quantitative signal differences. (C) Species-specific
binding despite conserved consensus sequences. (D) Binding only in S.
mikatae and S. bayanus. (E) Conserved binding with loss of consensus
sequences in one species. ChIp-chip enrichment signals are shown (log 2
ratios). Circles and squares represent matches to Tec1 PWM and Ste12
PWM, respectively. Triangles, nonconserved peaks; **, >2-fold difference
in peak signal intensity; *, >1.5-fold difference in peak signal

Friday, October 19, 2007

Electronic Versions of Papers

Could you please send me an electronic version of your paper "The packing density in proteins: standard radii and volumes", JMB 290, 1999, p253-266?

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

Thursday, October 18, 2007

How to input parameters in NuProt Calculator

I would like to use the NucProt Calculator for an RNA/protein mix, more exactly the genome of a virus plus several copies of its viral enzymes. I am not sure how I should input things in the program. Shall I introduce the sequence of the viral genome followed by those of the viral proteins?

The NucProt Packing-Eff calculator works on PDB structures NOT sequences, so they cannot mean that:

The NucProt PSV and Volume Calculator:
is not the best written CGI code that can take several sequences at once, but since I didn't understand HTTP GET and POST very well, I had it put all in the information in the GET rather than the POST, so there is a browser limit. I don't think I have write access anymore to this file.

Technically it can take several sequence in FASTA format though.

Wednesday, October 17, 2007

How to obtain datasets from interolog?

In the process of evaluating our "interologs" studies, we found that we need urgently the interaction datasets you used in Yu /et al. /(2004) /Genome Res/ *14*:1107-1118. We wish that we could acquire the datasets of fly (4768 interactions) and worm (410 interactions).

Please visit

Tuesday, October 9, 2007

Are there errors in "Relating 3D structures to protein networks provides evolutionary insights"?

After reading your paper "Relating 3D structures to protein networks provides evolutionary insights" which was published at SCIENCE in 2006, I have some questions about some details. In the third paragraph you said "proteins connected by simultaneously possible interactions are more likely to share the same function than are those connected by mutually exclusive ones", but the result which was shown in Table 1 looks like conversed. I also want to know the computing method of coexpression correlation and expression correlation, because I found their respective results which occur in Table1 and Table2 are also conversed.

You're right, also refer to our website, where we list this typo.

Data for Ste12 amd Tec1

Is your raw data avail for the tiling arrays of Ste12 and Tec1?

Please find it on GEO:

Wednesday, October 3, 2007

A tricky problem with PDB files

I've submitted this request a few times over the past month, never really looking too far into what might be causing the error. Today, however, I checked my pdb files and they have the same numbering and chain identification yet the error is the same. This is a pdb of an RNA under two conditions (one is the crystal structure, one is our model of an intermediate). Can you suggest any way forward?

The most common problems arise from use of a flavor of the PDB format that the morph server doesn't recognize, as you may be doing for the modelled structure. You could try submitting a truncated version of the the crystal structure (which I'm guessing you downloaded from the pdb) as structure 1, change a few coordinates, and submit that modified file as structure 2. This will give us a quick test to determine if it is your modelled structure that is causing the problem.

Monday, October 1, 2007

Morph Server functioning correctly?

Is the morph server functioning correctly? I’ve used it for several years for course projects but students are having difficulty with it this year. We have a new network system and I am trying to find out if it is on your end or ours where the problem lies.

The morph server has experienced an unexpected surge in popularity recently. We are discussing upgrading hardware and this should help. Also we will be investigating whether we have software issues that need to be addressed. I can tell you that new submissions are successfully being added daily, so the server does work. My suggestion for fast results is to try small proteins and ask for a small number of frames (maybe just 4 or so). Also we have three different morph engines as you may appreciate, so if one doesn't work you might try another the next day. Please don't flood our server with multiple submissions of similar proteins in a single day though.