Protein Simulation Using Fast Volume Preservation

  • Min Hong
  • David Osguthorpe
  • Min-Hyung Choi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3991)


Since empirical force fields computation requires a heavy computational cost, the simulation of complex protein structures is a time consuming process for predicting their configuration. To achieve fast but plausible global deformations of protein, we present an efficient and robust global shape based protein dynamics model using an implicit volume preservation method. A triangulated surface of the protein is generated using a marching cube algorithm in pre-processing time. The normal mode analysis based on motion data is used as a reference deformation of protein to estimate the necessary forces for protein movements. Our protein simulator provides a nice test-bed for initial screening of behavioral analysis to simulate various types of protein complexes.


Molecular Dynamic Simulation Adenylate Kinase Normal Mode Analysis Integration Time Step Surface Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Min Hong
    • 1
  • David Osguthorpe
    • 2
  • Min-Hyung Choi
    • 3
  1. 1.Division of Computer Science and EngineeringSoonchunhyang UniversityChungcheongnam-doKorea
  2. 2.PharmacologyUniversity of Colorado at Denver and Health Sciences CenterDenverUSA
  3. 3.Department of Computer Science and EngineeringUniversity of Colorado at Denver and Health Sciences CenterDenverUSA

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