Publications
This is Shikai's publications by categories in reversed chronological order. * denotes equal contribution
2022
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JBPExploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme modelJournal of Biological Physics 2022
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AbstractMechanism of translocation by bacteriophage T7 helicase gp4 using AWSEM-SuiteBiophysical Journal 2022
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PNASComputationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNAProceedings of the National Academy of Sciences 2022
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AbstractDeep learning-based prediction of electron density maps of proteinsBiophysical Journal 2022
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Nat CommUnleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfationNature Communications 2022
2021
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PLoS Comp BioOpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulationsPLoS computational biology 2021
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AbstractExploring the translocation mechanism of bacteriophage T7 helicaseBiophysical Journal 2021
2020
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NARAWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapesNucleic Acids Research 2020
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JCTCProtein structure prediction in CASP13 using AWSEM-SuiteJournal of Chemical Theory and Computation 2020
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JPCBProtein structure refinement guided by atomic packing frustration analysisThe Journal of Physical Chemistry B 2020
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IUCrJMolecular-replacement phasing using predicted protein structures from AWSEM-SuiteIUCrJ 2020
2019
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PNASForging tools for refining predicted protein structuresProceedings of the National Academy of Sciences 2019
2018
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Mol PharmacolIdentification of an oleanane-type triterpene hedragonic acid as a novel farnesoid X receptor ligand with liver protective effects and anti-inflammatory activityMolecular pharmacology 2018
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TrafficStructural insights into the nuclear import of the histone acetyltransferase males-absent-on-the-first by importin α1Traffic 2018
2017
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OncotargetFactors and pathways involved in capacitation: how are they regulated?Oncotarget 2017
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ChemBioChemA novel class of natural FXR modulators with a unique mode of selective co-regulator assemblyChemBioChem 2017