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Efficient rotamer elimination applied to protein side-chains and related spin glasses.

ABSTRACT: Folded proteins and spin glasses share various properties, such as seemingly random interactions between residues (spins), and one might presume that some generic behaviors of spin glasses would also be exhibited in a general way by proteins. But a comparison here shows that the side-chain conformation systems of apo-myoglobin and lysozyme are qualitatively different from specific closely related spin glass systems. This difference is manifest in the number of rotamers that can be identified as definitely not contributing to the global energy minimum. This identification is effected by using a significantly enhanced version of the Dead End Elimination theorem (Desmet, J., M. De Maeyer, B. Hazes, and I. Lasters. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature. 356:539-542), which is much more effective and efficient in eliminating rotamers. In several cases (for proteins, although not for spin glasses) this improved Dead End Elimination theorem succeeded in identifying the absolute global minimum of rotamer conformations, with no statistical uncertainty. The difference between protein and spin glass is due to correlations between the interactions of one residue pair with another pair, and probably will play an important role in the thermodynamic behavior of the protein system.

SUBMITTER: Goldstein RF

PROVIDER: S-EPMC1275854 | biostudies-other | 1994 May

REPOSITORIES: biostudies-other

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Efficient rotamer elimination applied to protein side-chains and related spin glasses.

Goldstein R F RF

Biophysical journal 19940501 5

Folded proteins and spin glasses share various properties, such as seemingly random interactions between residues (spins), and one might presume that some generic behaviors of spin glasses would also be exhibited in a general way by proteins. But a comparison here shows that the side-chain conformation systems of apo-myoglobin and lysozyme are qualitatively different from specific closely related spin glass systems. This difference is manifest in the number of rotamers that can be identified as ...[more]

PMID: 8061189

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Project description:INTRODUCTION: The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. METHODS: We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. RESULTS: We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. CONCLUSIONS: This parallel approach combines various sources of searching intelligence and energy functions to pack protein side chains. It provides a frame-work for combining different inaccuracy/usefulness objective functions by designing parallel heuristic search algorithms.

Dataset Information

Efficient rotamer elimination applied to protein side-chains and related spin glasses.

Publications

Efficient rotamer elimination applied to protein side-chains and related spin glasses.

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