ArticleBMC bioinformatics2014
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- De novo protein fold design through sequence-independent fragment assembly simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14.Proteins · 2021Article
- Article
- Identification of native protein structures captured by principal interactions.BMC bioinformatics · 2019Article
- A simple neural network implementation of generalized solvation free energy for assessment of protein structural models.RSC advances · 2019Article
- Role of solvent accessibility for aggregation-prone patches in protein folding.Scientific reports · 2018Article
- Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction.BMC bioinformatics · 2017Article
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2 authors.
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Abstract
backgroundMultibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures.
resultsIn this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality.
conclusionsA new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.
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