NPSA: An Implicit Solvent Model for Protein Docking and Unfolding Simulations

Ting Wang & Rebecca Wade

EML Research gGmbH, 69118 Heidelberg, Germany

We have developed an implicit solvent model called NPSA particularly for protein simulations because including explicit water molecules in calculations can dramatically increase the computing time and the storage space. The NPSA model is a modification of a distance-dependent dielectric model plus a solvent accessible surface term. Charged residues are neutralized but with high polarity. Ting Wang and Rebecca Wade, Proteins. 50: 158-169, 2003. Imprint/Privacy