Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses حسب Dominykas Lukauskis (14143149)

"…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …"

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses حسب Dominykas Lukauskis (14143149)

"…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …"

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses حسب Dominykas Lukauskis (14143149)

"…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …"

Properties of the 14 features that were used for building the model. حسب Aimilia-Christina Vagiona (17584758)

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Z scores waterfall plot for the DLPFC cohort. حسب Erica A. K. DePasquale (11851483)

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Changes in phosphorylation at reporter peptides in female vs. male DLPFC. حسب Erica A. K. DePasquale (11851483)

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Predicted kinases and distributions for female vs. male (HPC). حسب Erica A. K. DePasquale (11851483)

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Observed frequency of selected kinases relative to expected random sampling distribution in female vs. male DLPFC. حسب Erica A. K. DePasquale (11851483)

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Robustness analysis of capturing upstream kinase scores under different signal-to-noise ratio (SNR) values. حسب Erica A. K. DePasquale (11851483)

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Principal Component Analysis (PCA) of the independent dataset from the HPC cohort. حسب Erica A. K. DePasquale (11851483)

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Correlation analysis between the DLPFC and HPC cohorts. حسب Erica A. K. DePasquale (11851483)

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Global serine-threonine kinase activity in female vs. male DLPFC. حسب Erica A. K. DePasquale (11851483)

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Workflow overview illustrating the primary steps of the KRSA pipeline. حسب Erica A. K. DePasquale (11851483)

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Venn diagrams showing overlap of the total of overrepresented/underrepresented kinases for both cohorts. حسب Erica A. K. DePasquale (11851483)

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Predicted kinases and distributions for female vs. male (DLPFC). حسب Erica A. K. DePasquale (11851483)

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Convergence curves of the two algorithms in the Griewank function. حسب Huazan Liu (9137461)

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Convergence curves of different algorithms on the benchmark functions. حسب Aihua Guo (13267712)

Convergence curves of the two algorithms in the Rastrigin function. حسب Huazan Liu (9137461)

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ROC curves of CNN + LSTM model and traditional algorithms. حسب Zhongzhong Guo (12133402)

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Supplemental Tables S1 and S2 for Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks حسب Diana Murray (16859046)

"…Biological insights derived from the subnetworks, including the annotation of proteins of unknown function, are discussed in detail. …"