ArticlePloS one2012
BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 44 citations in OpenAlex.
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- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
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- Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking.Computational and structural biotechnology journal · 2019Article
- Protein structure aids predicting functional perturbation of missense variants inComputational and structural biotechnology journal · 2019Article
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- GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.Nucleic acids research · 2018Article
- Enhanced stability of a chimeric hepatitis B core antigen virus-like-particle (HBcAg-VLP) by a C-terminal linker-hexahistidine-peptide.Journal of nanobiotechnology · 2018Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.Journal of chemical theory and computation · 2017Article
- Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints.Proteins · 2017Article
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- Variability of Protein Structure Models from Electron Microscopy.Structure (London, England : 1993) · 2017Article
- Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification.PloS one · 2017Article
- Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning.PloS one · 2017Article
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
- Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX.Journal of structural biology · 2016Article
- Characterization of the Domain Orientations of E. coli 5'-Nucleotidase by Fitting an Ensemble of Conformers to DEER Distance Distributions.Structure (London, England : 1993) · 2016Article
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6 authors at 1 institution in 1 country.
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Abstract
The topology of most experimentally determined protein domains is defined by the relative arrangement of secondary structure elements, i.e. α-helices and β-strands, which make up 50-70% of the sequence. Pairing of β-strands defines the topology of β-sheets. The packing of side chains between α-helices and β-sheets defines the majority of the protein core. Often, limited experimental datasets restrain the position of secondary structure elements while lacking detail with respect to loop or side chain conformation. At the same time the regular structure and reduced flexibility of secondary structure elements make these interactions more predictable when compared to flexible loops and side chains. To determine the topology of the protein in such settings, we introduce a tailored knowledge-based energy function that evaluates arrangement of secondary structure elements only. Based on the amino acid C(β) atom coordinates within secondary structure elements, potentials for amino acid pair distance, amino acid environment, secondary structure element packing, β-strand pairing, loop length, radius of gyration, contact order and secondary structure prediction agreement are defined. Separate penalty functions exclude conformations with clashes between amino acids or secondary structure elements and loops that cannot be closed. Each individual term discriminates for native-like protein structures. The composite potential significantly enriches for native-like models in three different databases of 10,000-12,000 protein models in 80-94% of the cases. The corresponding application, "BCL::ScoreProtein," is available at www.meilerlab.org.
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