Prof. Martin Stone has decided to discontinue the Indiana Dynamics Database due to lack of interest among NMR researchers (see a message
Prof. Stone's website below). Entries from the database are still available on
the web. On behalf of BioNMR.com community, I would like to thank Prof. Stone for his efforts to build and maintain this database.
It is unfortunate that publishers of articles about NMR-derived dynamics do not require submission of NMR experimental data and calculated parameters of protein dynamics into a public database, such as the Indiana Dynamics Database and BMRB. As a result, scientists, who need to use published results of NMR dynamics experiments from other labs, still have to spend their time converting article pictures into numbers or trying to obtain the numbers (not always successfully) from authors of the NMR dynamics papers.
The ability to characterize protein dynamics is a strong and distinct feature of modern NMR spectroscopy. Why do we find it necessary to deposit NMR assignments into the BMRB database and solution structures into the PDB database, but treat NMR dynamics data as some scientific junk that is not worth to be available in a public database?
Message from
Prof. Stone's website:
The IDD was established in 2000 with the goal of promoting the dissemination of NMR relaxation and derived dynamics data. Due to the limited number of submissions to the database we have reluctantly decided not to continue maintaining this service. We apologize for any inconvenience that this may cause.
We are posting on this web site the IDD data files for the early submissions to the database (all 15N relaxation and dynamics data sets). A statistical analysis of these data is described in the following publication.
Goodman, J.L., Pagel, M.D., and Stone, M.J. Relationships Between Protein Structure and Dynamics from a Database of NMR-Derived Backbone Order Parameters. J. Molec. Biol. (2000) 295, 963-978.
For each protein listed in the left-hand panel, we provide two ASCII text files.
(1) The header file contains general information about the protein, the available data, and the method of data analysis. Each comment line (beginning with ‘#’) indicates the type of information in the following line(s).
(2) The data file contains the relaxation and dynamics parameters for the protein, separated into columns. Line 1 of this files gives the protein name. Line 3 identifies the type of data (space delimited) in each row for the remainder of the file. Notation is as follows:
Res = residue number
AA = amino acid type
T1(ms) = T1 relaxation time in milliseconds
dT1 = standard error in the T1 value
etc.
Linear Mode
