Creative Biolabs offers customers rotamer library construction services for molecular modeling and protein design.
More than 100,000 protein structures have been determined and stored in the Protein Data Bank (PDB). However, accurate structural modeling of unknown protein structures remains one of the most challenging problems in molecular biology. Protein side chains prefer distinct conformations (called rotamers) according to organic chemistry first principles. Modeling the protein structure involves determining the optimum side-chain conformation as well as backbone geometry. It is important for understanding the protein function because the activity is often structure-dependent. As a concise description of side-chain conformational preferences, rotamer libraries are typically derived from a large sample of crystal structures using filters to remove poor quality data and statistical techniques to improve the data in low frequency regions, containing information about the protein side-chain conformation like the frequency of a certain conformation and the variance on dihedral angle means or modes.
Figure 1: Rotamers with different side-chain conformations (P. Douglas Renfrew et al., 2014)
We have created a backbone-independent rotamer library from 298K simulations of the initial release of 188 proteins in the Dynameomics database. Structures from molecular dynamics have two advantages over experimental data. First, structures have perfect information. There is no ambiguity about coordinates from weak electron density, particularly for large residues on the surface of the protein. Second, the structures are taken in solution, avoiding possible biases from the crystalline environment.
Depending on the richness of contextual information provided, there can be a few kinds of rotamer libraries. Backbone independent rotamer libraries consider only amino acid specific context and the probabilities are given for rotamers of different amino acids. To increase the discriminative power of the backbone independent libraries, the backbone dependent rotamer libraries have been introduced, which take into consideration the local backbone context through the ϕ and ψ angles along with the amino acid information. Theoretically, the more context-specific information the library can encode, the more precise rotamer choices it can deliver. A protein-dependent rotamer library can be built with the detailed backbone atom coordinates of a specific protein, to better consider their interactions with the surrounding environments. We can help you build such libraries, which can be widely used in protein structure prediction, protein design and structure refinement.