The Fold List page contains a description of how we generated our consensus domain dictionary (CDD) from the SCOP, CATH, and Dali domain dictionaries. We describe both the methods for generating the dictionary and the rationale behind it's generation. We also include summary statistics of the CDD and it's inputs.

Browse and search Dynameomics targets for both the 2009 and 2003 consensus sets by image or name; determine a simulated target that is the same family as your protein of interest.

Single Nucleotide Polymorphisms (SNPs) are mutations that involve a single nucleotide mutation in an organism's genetic sequence. In humans, they occur approximately once every 300 nucleotide bases, making them our most common source of genetic variation. When these mutations result in an amino acid change in the transcribed protein, they can be responsible for the protein's altered function. SNPs, and their associated change in protein function, are known to cause a variety of human diseases ranging from Parkinson’s disease to epilepsy. Mutations in tumor protein 53 (p53) are correlated with approximately 50% of all cancers.

The Dynameomics database contains simulations of 31 different proteins, including wildtype and mutant simulations. In all, we have over 200 single-point mutations simulations available for analysis.

Our simulation libraries contain a wealth of information about basic amino-acid structural properties. The primary library is Dynameomics, containing simulations of over 800 proteins, which serves to study residues in their protein context. This is supplemented by a library of simulations of the peptide GGXGG, where X is each amino acid. This library serves for investigation of the intrensic propensities of amino-acids in a minimal protein context.

On the SLIRP page, three data sets are available:

• Dynamical Fragment Library from Dynameomics Simulations
• Rotamer Library from Dynameoimcs and GGXGG
• Detailed Properties of GGXGG Peptide Simulations

The Methods pages include a description of the criteria we use to select protein targets for simulation from our Consensus Domain Dictionary. We provide an overview of our simulation software and protocols. We describe our quality control efforts to asses the stability of proteins in their native state simulation and give the details of our standard analysis suite.

The Dynameomics data warehouse is based on SQL Server 2005 and 2008 and contains over 55TB of MD simulation and analysis data. These data are distributed across 7 primary servers that range in size from 7.5 TB to 25 TB of storage. Native state simulation data for the top 100 Dynameomics targets, SNP targets, and the GGXGG Peptides can be browsed using this site. You can also request  a SQL Login to run your own queries, and a web services interface is being developed to allow direct access using SOAP.

The Data mining section describes in detail how a number of large scale data analyses were conducted on the database. These analyses include flexibilty calculations, wavelet calculations, transition state mining and reaction coordinate calculations. Examples code (SQL and Mathematica) of how to conduct these analyses are also given in this section.

Contact us with questions or comments about the website at dynameomics_info@uw.edu.

If you are interested in accessing the data on this site directly within our database, you can request a login. Please download the form and return it via fax or scan it and email it to dynameomics_info@uw.edu.

Download Request Form Here