Publications

  1. Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization  I. Global Energy Minimization of Surface Loops, M.J.Dudek, and H.A.Scheraga, J.Comput.Chem., 11, 121–151 (1990).
  2. Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, M.J.Dudek, and J.W.Ponder, J.Comput.Chem., 16, 791–816 (1995).
  3. The impact of atomic dipoles and quadrupoles on calculated crystal structures and sublimation energies of model amide compounds., M.J.Dudek, online document, prepared August 1995.
  4. Protein Structure Prediction Using a Combination of Sequence Homology and Global Energy Minimization  II. Energy Functions, M.J.Dudek, K.Ramnarayan, and J.W.Ponder, J.Comput.Chem., 19, 548–573 (1998).
  5. Application of a Detailed Energy Surface to Homology Modeling of the ω-Conotoxin Family, M.J.Dudek, and K.Ramnarayan, Proceedings of the Seventeenth American Peptide Symposium, 428–429 (2001).
  6. igor, a Simple Integrable Model of a Polypeptide Chain  I. Model Description, M.J.Dudek, online document, prepared March 2007.
  7. A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability, M.J.Dudek, Proteins, 82, 2497–2511 (2014).
  8. igor, a Simple Integrable Model of a Polypeptide Chain, M.J.Dudek, online document, prepared June 2024.
  9. Guided Trajectory Search Through the Space of Generalized Coordinates for a Rigid Geometry Mechanical System, M.J.Dudek, online document, prepared June 2024.