AMBER8:

• NPSA:
  This implicit solvent model for protein simulations (with Neutralized, Polarized ionizable side chains with a solvent-accessible Surface Area-dependent term) is described in:
  • T. Wang and R. C. Wade. Implicit Solvent Models for Flexible Protein-protein Docking by Molecular Dynamics Simulation Proteins: Str., Function and Genetics, 50, 158-169 (2003). doi:10.1002/prot.10248
  • T. Wang and R. C. Wade. Force Field Effects on a beta-sheet Protein Domain Structure in Thermal Unfolding Simulations. J. Chem. Theory Comput., (2006) 2, 140 -148. doi:10.1021/ct0501607
• RAMD:
  The Random Acceleration Molecular Dynamics (RAMD) method can be used to carried out molecular dynamics simulations with an additional randomly oriented force applied to the center of mass of one molecule in the system. It can be used for example to identify egress routes for a ligand from a buried protein binding site. RAMD and its applications are described in:
  • Luedemann, S.K., Lounnas, V. and R. C. Wade. How do Substrates Enter and Products Exit the Buried Active Site of Cytochrome P450cam ? 1. Random Expulsion Molecular Dynamics Investigation of Ligand Access Channels and Mechanisms. J Mol Biol, 303:797-811 (2000). doi:10.1002/jmbi.2000.4154
  • Luedemann, S.K., Gabdoulline,R.R., Lounnas, V. and R. C. Wade. Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms. Internet Journal of Chemistry, 4, 6 (2001). http://www.ijc.com/articles/2001v4/6/
  • Winn,P., Luedemann, S.K., Gauges,R., Lounnas, V. and R. C. Wade. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine PNAS, 99, 5361-5366 (2002). Full text
  • Schleinkofer, K., Sudarko, Winn,P., Luedemann, S.K. and R. C. Wade. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling? EMBO Reports, 6, 584-589 (2005).doi:10.1038/sj.embor.7400420
  • Wang, T., Duan, Y. Chromophore channeling in the G-protein coupled receptor rhodopsin.
    J. Am. Chem. Soc. 129, 6970-6971 (2007).doi:10.1021/ja0691977