Structural Library of Intrinsic Residue Propensities (SLIRP)
The Daggett Lab has created a fragment library from snapshots of the
Dynameomics simulation database. The library is comprised of 3-9
residue fragments and includes N, Cα, Cβ, C, and O atoms
of reach residue. The complete library consists of over 1.3 million
fragments of each length. We have clustered the fragments to reduce
that size significantly without losing structural diversity.
The library was created to be combined with our Rotamer library in order
to build missing residues into Dynameomics targets for simulation.
The approach uses novel fragment selection and insertion algorithm
which is currently in preparation for publication.
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.
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.