Creative BioMart's extensive experience in solving protein side chain stacking problems and predicting protein side chain structures enables us to provide rotamer libraries construction services for molecular modeling and protein design to accelerate your projects. Our rotamer library keeps the side chain conformation space as small as possible to reduce computer memory requirements. It has been widely used in protein structure prediction, protein design and structure refinement.

Although the three-dimensional structures of more than 50,000 proteins have been determined and recorded in the Protein Data Bank (PDB) to date, precise structural modeling of unknown proteins remains one of the most challenging problems in molecular biology. Proteins contain backbone and side chain components. The key to protein structure modeling is to determine the optimal side chain conformation and main chain geometry, but it is difficult to predict the complete protein structure at the same time. Therefore, a key component of many protein design programs is to focus on predicting and modeling side chain conformations for a given backbone structure by representing side chains as rotamers. The rotamer library will result in improved performance compared to models based on continuous variation of the dihedral angle. Furthermore, the conformations contained in the rotational molecular library correspond well to the calculated energy minima in the form of isolated dipeptides.

Fig 1. Rotamer and amino acid interaction energy graph. (Jaramillo A, et al., 2001)

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Rotary protein repertoires can be backbone-independent or secondary-structure-dependent backbone conformations. The rotamer library quantitatively summarizes the current knowledge of experimentally determined structures, containing estimated probabilities of discrete conformations of side-chain dihedral angles calculated from the structure database. Creative BioMart has successfully constructed rotamer libraries for molecular modeling and protein design. Depending on how much context information is encoded, our successfully constructed rotamer library contains:

• Trunk-independent rotamer library

Only sequence information is encoded, and probabilities for rotamers of different amino acids are given. But the discriminative power of this library is not sufficient to eliminate a sufficient number of rotamer selections.

• Backbone-dependent rotamer library

The local backbone context is taken into account by φ and ψ angles and amino acid information. This library is able to improve the accuracy of sidechain predictors equipped with a global optimizer over the energy function landscape and guide them to avoid local minima.

Rotamers libraries have become an important part of protein design toolboxes. Our scientists are familiar with methods for creating rotamer libraries, methods for evaluating assumptions made when utilizing rotamers, and methods for characterizing the performance of the resulting rotamer libraries, which can be used for unknown proteins Accurate structural modeling of the best solution.

If you have any special requirements about our rotamer libraries construction services, please feel free to contact us . We are looking forward to working together with your attractive projects.

References

1. Renfrew P D, Craven T W, Butterfoss G L, et al.. (2014) A rotamer library to enable modeling and design of peptoid foldamers[J]. Journal of the American Chemical Society. 136 (24): 8772-8782.
2. Dunbrack Jr R L. (2002) Rotamer libraries in the 21st century[J]. Current opinion in structural biology. 12(4): 431-440.
3. Jaramillo A, Wernisch L, Héry S, et al. (2001) Automatic procedures for protein design[J]. Combinatorial chemistry & high throughput screening. 4(8): 643-659.

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