The Daggett Lab has created fragment libraries from both the Dynameomics data
warehouse and Protein Data Bank (PDB). The library is comprised of 3 to 22
residue fragments and includes N, Cα, Cβ, C, and O atoms
of each residue. The complete library consists of approximately one billion
Our fragment libraries were created to identify, rank and retrieve protein structure fragments for protein loop structure
prediction. Dynameomics fragment structures supplement crystal structure fragment conformations
to improve loop predictions without being dependent on sequence homology. The fragment libraries
also integrate with our rotamer libraries. Several interfaces are available to take
advantage of these resources, described in detail here.
Rotamer libraries describe the conformational preferences of amino-acid
side chains and are a common tool for structural biologists.
The Daggett Lab has compiled a backbone-independent rotamer
library from the 188 native-state protein simulations currently
comprising the Dynameomics database. The library contains frequencies
and χ angle preferences for each rotamer.
The 2011 rotamer library has been updated to include the full set of 807 native-state
protein domain simulations in the Dynameomics database. In addition, backbone-dependent and
secondary structure dependent libraries have been added. The libraries are available for download, upon request (contact us for a backbone-dependent, backbone-independent, and secondary-structure-dependent rotamer library).
To study the inherent structural propensities of amino acids in a minimal protein context,
Daggett lab has simulated each residue in a model peptide -- Ac-GGXGG-NH2,
where X is each of the 20 amino acids, including protonation variants. Each residue is
simulated for 100 ns at 298 K in explicit solvent. Some residues have multiple simulations
to gaugue conformational sampling. The total simulation time is 3.8 microseconds. General
analysis of the simulations is available here and the simulations are also included in our
broader main-chain and side-chain analyses. The simulations were performed
according to our standard Dynameomics simulation protocol.
D-amino acids have properties that make them desirable drug and vaccine targets.
Using a GGXGG host-guest pentapeptide system, we performed exhaustive sampling of
the conformational propensities for both L- and D- amino acids. Knowledge of such
propensities can inform peptide design. These simulations included D-allo-isoleucine
and D-allo-threonine, which are the forms of isoleucine and threonine obtained
in vivo through α-epimerization, where the original side chain chiralities are retained.
The total simualtion time 6.6 μ-seconds. The conformational propensities of all
the amino acids are availalable here.
The simulations were again performed according to our standard Dynameomics Protocol.