Smooth orientation-dependent scoring function for coarse-grained protein quality assessment

Mikhail Karasikov 1, 2 Guillaume Pagès 2 Sergei Grudinin 2
2 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
Abstract : Motivation: Protein quality assessment (QA) is a crucial element of protein structure prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at ranking predicted protein models to select the best candidates. The assessment can be performed based either on a single model or on a consensus derived from an ensemble of models. The latter strategy can yield very high performance but substantially depends on the pool of available candidate models, which limits its applicability. Hence, single-model QA methods remain an important research target, also because they can assist the sampling of candidate models.
Results: We present a novel single-model QA method called SBROD. The SBROD (Smooth Backbone-Reliant Orientation-Dependent) method uses only the backbone protein conforma-tion, and hence it can be applied to scoring coarse-grained protein models. The proposed method deduces its scoring function from a training set of protein models. The SBROD scoring function is composed of four terms related to different structural features: residue-residue orientations, contacts between backbone atoms, hydrogen bonding, and solvent-solute interactions. It is smooth with respect to atomic coordinates and thus is potentially applicable to continuous gradient-based optimization of protein conformations. Furthermore, it can also be used for coarse-grained protein modeling and computational protein design. SBROD proved to achieve similar performance to state-of-the-art single-model QA methods on diverse datasets (CASP11, CASP12, and MOULDER).
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Mikhail Karasikov, Guillaume Pagès, Sergei Grudinin. Smooth orientation-dependent scoring function for coarse-grained protein quality assessment. Bioinformatics, Oxford University Press (OUP), 2019, 35 (16), pp.2801-2808. ⟨10.1093/bioinformatics/bty1037⟩. ⟨hal-01971128⟩

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