Supplemental Material for

VESPER: global and local cryo-EM map alignment using local density vectors.

Xusi Han,a Genki Terashi,a Charles Christoffer,b Siyang Chen,b Daisuke Kiharaa,b

a Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
b Department of Computer Science, Purdue University, West Lafayette, IN 47907

Supplemental Dataset

    The VESPER program is available on Github Page.

  • Benchmark dataset of Joseph, Agnel Praveen, et al. "Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy." Journal of Structural Biology 199.1 (2017): 12-26. (20 maps).
    • Rotation, Translation, and RMSD tables (100 superimpositions per target.)
      • 1-9th columns: Rotation Matrix (3*3)
      10-12th columns:Translation Vector (3)
      13th column: log(ALCPS)
      14th column: Angle difference between the reference and current fit (theta)
      15th column: Distance of Translation between the reference and current fit (r)
      16th column: RMSD
    • Reference PDB model (Superimposed)
    • 18 metrics and DOT score tables
      Filename is formatted as [emid1]_[emid2]_[Score Type].dat
      The first row shows emid1 and emid2. From the second row, 1st column is the score. 2nd column is the model ID.
        Score types
        CCCGlobal Cross-Correlation
        SCCCLocal Cross-Correlation
        SMOCSegment based Mander' Overlap Coefficient
        LMILocal Mutual Information
        NMINormalized Mutual Information
        CDTChamfer Distance of surface based on a density Threshold
        CDAChamfer Distance of surface based on All points on the contour surface
        CDMChamfer Distance of surface based on Mean filter
        CDT_GDTWeighted CDT
        CDA_GDTWeighted CDA
        CDM_GDTWeighted CDM
        NVTNormal Vector score at surface points at a density Threshold
        NVANormal Vector score at surface points at the contour surface
        NVMNormal Vector score at surface points at Mean filter
        OVROverlap score
        SCCC_OVCombined score of SCCC and OV
        SMOV_OVCombined score of SMOV and OV
        LMI_OVCombined score of LMI and OV
        DOTUnit-vector based score in VESPER

  • Benchmark dataset of Partial map alignment (57 targets)

Reference

Han, Xusi, Genki Terashi, Charles Christoffer, Siyang Chen, and Daisuke Kihara. "VESPER: global and local cryo-EM map alignment using local density vectors." Nature Communications 12, no. 1 (2021): 1-12.

Contact Information

If you have any questions or suggestions, please feel free to contact us at:

Daisuke Kihara (dkihara@purdue.edu)

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