Lin Song

Contact information
email: song21@llnl.gov

 

  

 

Education/Experience

Ph.D., Chemistry, Michigan State University, 2014-2020

BS, Chemistry, Xiamen University, 2009-2013

 

Research

I’m interested in using molecular dynamics and QM/MM to understand enzyme catalysis mechanisms as well as design novel drug candidates based on that understanding. I’m also interested in applying free-energy studies to improve drug potency.  Developing molecular dynamics force fields for metal ions is another area of interest.

 

Publications

  1. Pei, J., Song, L. F., & Merz Jr, K. M. (2021). FFENCODER-PL: Pair Wise Energy Descriptors for Protein-Ligand Pose Selection. Journal of Chemical Theory and Computation.
  2. Li, Z., Song, L. F., Li, P., & Merz Jr, K. M. (2021). Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of chemical theory and computation, 17(4), 2342-2354.
  3. Sengupta, A., Li, Z., Song, L. F., Li, P., & Merz Jr, K. M. (2021). Parameterization of Monovalent Ions for the Opc3, Opc, Tip3p-Fb, and Tip4p-Fb Water Models. Journal of chemical information and modeling, 61(2), 869-880.
  4. Song, L. F., & Merz Jr, K. M. (2020). Evolution of alchemical free energy methods in drug discovery. Journal of Chemical Information and Modeling, 60(11), 5308-5318
  5. Pei, J., Song, L. F., & Merz Jr, K. M. (2020). Pair Potentials as Machine Learning Features. Journal of chemical theory and computation, 16(8), 5385-5400.
  6. Li, Z., Song, L. F., Li, P., & Merz Jr, K. M. (2020). Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of chemical theory and computation, 16(7), 4429-4442.
  7. Song, L. F., Sengupta, A., & Merz Jr, K. M. (2020). Thermodynamics of Transition Metal Ion Binding to Proteins. Journal of the American Chemical Society, 142(13), 6365-6374.
  8. Song, L. F., Lee, T. S., Zhu, C., York, D. M., & Merz Jr, K. M. (2019). Using AMBER18 for Relative Free Energy Calculations. Journal of chemical information and modeling, 59(7), 3128-3135.
  9. Pei, J., Zheng, Z., Kim, H., Song, L. F., Walworth, S., Merz, M. R., & Merz Jr, K. M. (2019). Random Forest Refinement of Pairwise Potentials for Protein–Ligand Decoy Detection. Journal of chemical information and modeling, 59(7), 3305-3315.
  10. Song, L. F., Bansal, N., Zheng, Z., & Merz, K. M. (2018). Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge. Journal of computer-aided molecular design, 32(10), 1013-1026.
  11. Zheng, Z., Pei, J., Bansal, N., Liu, H., Song, L. F., & Merz, K. M. (2018). Generation of Pairwise Potentials Using Multi-Dimensional Data Mining. Journal of Chemical Theory and Computation.
  12. Bansal, N., Zheng, Z., Song, L. F., Pei, J., & Merz Jr, K. M. (2018). The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation. Journal of the American Chemical Society, 140(16), 5434-5446.
  13. Pan, L. L., Song, L. F., Miao, Y., Yang, Y., & Merz Jr, K. M. (2017). Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?. Biochemistry, 56(24), 2995-3007.
  14. Wang, Y. C., Lai, Y. J., Song, L., Zhou, Z. Y., Liu, J. G., Wang, Q., ... & Rauf, M. (2015). S‐Doping of an Fe/N/C ORR Catalyst for Polymer Electrolyte Membrane Fuel Cells with High Power Density. Angewandte Chemie, 127(34), 10045-10048.
  15. Li, P., Song, L. F., & Merz Jr, K. M. (2015). Systematic parameterization of monovalent ions employing the nonbonded model. Journal of chemical theory and computation, 11(4), 1645-1657.
  16. Li, P., Song, L. F., & Merz Jr, K. M. (2014). Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. The Journal of Physical Chemistry B, 119(3), 883-895.
  17. Wang, Q., Zhou, Z.Y., Lai, Y.J., You, Y., Liu, J.G., Wu, X.L., Terefe, E., Chen, C., Song, L., Rauf, M., Tian, N. & Sun, S.G., (2014). Phenylenediamine-based FeN x/C catalyst with high activity for oxygen reduction in acid medium and its active-site probing. Journal of the American Chemical Society, 136(31), pp.10882-10885.