ArticleProtein science : a publication of the Protein Society2008
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
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- Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.International journal of molecular sciences · 2022Article
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- DE-STRESS: a user-friendly web application for the evaluation of protein designs.Protein engineering, design & selection : PEDS · 2021Article
- Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off.Computational and structural biotechnology journal · 2021Article
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- Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.The EMBO journal · 2020Article
- An information gain-based approach for evaluating protein structure models.Computational and structural biotechnology journal · 2020Article
- Designing a less immunogenic nattokinase from Bacillus subtilis subsp. natto: a computational mutagenesis.Journal of molecular modeling · 2019Article
- DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.Journal of cheminformatics · 2019Article
- VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes.Nucleic acids research · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
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- Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.Biophysical journal · 2018Article
5 more citing papers are in PubMed but not listed here.
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Abstract
One of the common methods for assessing energy functions of proteins is selection of native or near-native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all-atom statistical energy functions, DFIRE (distance-scaled, finite, ideal-gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence-position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short-range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 A global root-mean-squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.
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