1. Home

BioChemSIM is a package that can be used for analysis of differential and integral molecular properties (hydrophobicity, electrostatics etc.) and molecular dynamics. Input is a 3D structure of molecules (pdb or pqr format) from which it generates the SES (Solvent Excluded Surface) using Gaussian blurring and extracts a surface (triangular or quadrilateral) and volume (tetrahedral or hexahedral) mesh.

For more pictures, animations, and interactive viz. of macromolecular structures using BioChemSIM, please visit CVC Gallery.


  • BioChemSIM is developed using C++ and QT.
  • Supports 3D structure of molecules (pdb or pqr format).


  • We have a tutorial to familiarize you with BioChemSIM.

References, available on CVC Publications

  • Y. Zhang, C. Bajaj
    Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
    Computer Methods in Applied Mechanics and Engineering, Volume 195, Issues 9-12, 1 February 2006, Pages 942-960. (pdf) (abstract)
  • Y. Zhang, C. Bajaj, B. Sohn
    3D Finite Element Meshing from Imaging Data
    Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194, 48-49, 5083-5106, 2005. (pdf) (abstract)
  • Y. Zhang, G. Xu, C. Bajaj
    Quality Meshing of Implicit Solvation Models of Biomolecular Structures
    The special issue of Computer Aided Geometric Design (CAGD) on Applications of Geometric Modeling in the Life Sciences, Volume 23, Issue 6, August 2006, Pages 510-530. (pdf) (abstract)
  • Y. Zhang, C. Bajaj, G. Xu
    Surface Smoothing and Quality Improvement of Quadrilateral/Hexahedral Meshes with Geometric Flow
    Proceedings of 14th International Meshing Roundtable, pp. 449-468. San Diego, CA. September 11-14, 2005. (pdf)