Valence optimization and angle improvement for molecular surface remeshing

Dawar Khan*, Alexander Plopski, Yuichiro Fujimoto, Masayuki Kanbara, Zhanglin Cheng, Hirokazu Kato

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Molecular surface mesh generation plays a vital role in molecular modeling and visualization. However, meshes extracted directly from Protein Data Bank files have several issues such as small and large triangles, redundant elements, self-intersections, and irregular vertices. The state-of-the-art mesh improvement methods often fail to deal with these issues. In this paper, we present a novel method for valence optimization and angle improvement. For valence optimization, we remove the bad valence vertices with its neighbor triangle making regular holes in the mesh. The holes are filled in a careful manner to improve their valences as well as angle quality. We also use a segmentation-based surface remeshing which segments the mesh into random segments and then each segment is independently remeshed. In addition, a point insertion scheme is applied to minimize the ratio of obtuse triangles. Experimental results show that our method not only improves the maximal and minimal angles to an angle bound of [30∘120∘] but also improves the vertices’ regularity, reduces the ratio of obtuse triangles, preserves the area and volume, and always succeeds with downstream applications.

Original languageEnglish (US)
Pages (from-to)2355-2368
Number of pages14
JournalVisual Computer
Issue number10-12
StatePublished - Oct 1 2020


  • Mesh quality
  • Molecular modeling
  • Molecular surface remeshing
  • Valence optimization

ASJC Scopus subject areas

  • Software
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design


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