Dependence of DNA Polymerase Replication Rate on External Forces: A Model Based on Molecular Dynamics Simulations, by I. Andricioaei, A. Goel, D. Herschbach, and M. Karplus, Biophys. J. 87, 1478-1497 (2004).
Hidden Complexity of Free Energy Surfaces for Peptide (Protein) Folding, by S. Krivov and M. Karplus, Proc. Natl. Acad. Sci. USA 101, 14766-14770 (2004).
The Role of Sequence and Structure in Protein Folding Kinetics: the Diffusion-Collision Model Applied to Proteins L and G, by S. A. Islam, M. Karplus, and D. L. Weaver, Structure 12, 1833-1845 (2004).
Calculation of the Aqueous Solvation Energy and Entropy, as well as Free Energy, of Simple Polar Solutes, by S. Wan, R. H. Stote, and M. Karplus, J. Chem. Phys. 121, 9539-9548 (2004).
Protein Structural Transitions and their Functional Role, by M. Karplus, Y. Q. Gao, J. Ma, A. van der Vaart, and W. Yang, Phil. Trans. R. Soc. A 363, 331-355 (2005).
Electrostatic Energies and Forces Computed Without Explicit Interparticle Interactions: A Linear Time Complexity Formulation, by R. J. Petrella and M. Karplus, J. Comput. Chem. 26, 755-787 (2005).
Structure of a Repair Enzyme Interrogating Undamaged DNA Elucidates Recognition of Damaged DNA, by A. Banerjee, W. Yang, M. Karplus and G. Verdine, Nature 434, 612-618 (2005).
Folding Time Distributions as an Approach to Protein Folding Kinetics, by S. F. Chekmarev, S. V. Krivov and M. Karplus, J. Phys. Chem. B 109, 5312- 5330 (2005).
Simulation of Conformational Transitions by the Restricted Perturbation- Targeted Molecular Dynamics (RP-TMD) Method, by A. van der Vaart and M. Karplus, J. Chem. Phys. 122, 114903.1-114903.6 (2005).
What Contributions to Protein Side-chain Dynamics are Probed by NMR Experiments? A Molecular Dynamics Simulation Analysis, by R. B. Best, J. Clarke, and M. Karplus, J. Mol. Biol. 349, 185-203 (2005).
Design, Synthesis and Biological Evaluation of HSP90 Inhibitors Based on Conformational Analysis of Radicicol and Its Analogues, by E. Moulin, V. Zoete, S. Barluenga, M. Karplus, and N. Winssinger. J. Am. Chem. Soc. 127, 6999-7004 (2005).
Molecular Dynamics and Protein Function, by M. Karplus and J. Kuriyan, Proc. Natl. Acad. Sci. USA 102, 6679-6685 (2005).
Normal Mode Calculations of Icosahedral Viruses with Full Dihedral Flexibility by Use of Molecular Symmetry, by H. W. T. van Vlijmen and M. Karplus, J. Mol. Biol. 350, 528-542 (2005).
Role of Conformational Heterogeneity in Domain Swapping and Adapter Function of the Cks Proteins, by M. A. Seeliger, M. Spichty, S. E. Kelly, M. Bycroft, S.M.F. Freund, M. Karplus, and L. S. Itzhaki, J. Biol. Chem. 280, 30448-30459 (2005).
Transition State Contact Orders Correlate with Protein Folding Rates, by E. Paci, K. Lindorff-Larsen, C. M. Dobson, M. Karplus, and M. Vendruscolo, J. Mol. Biol. 352, 495-500 (2005).
Study of the Insulin Dimerization from Binding Free Energy Calculations and Per-Residue Free Energy Decomposition, by V. Zoete, M. Meuwly, and M. Karplus, Proteins: Structure, Function & Bioinformatics 61, 79-93 (2005).
Large Amplitude Conformational Change in Proteins with a Plastic Network Model: Adenylate Kinase and a Subunit of GroEL, by P. Maragakis and M. Karplus, J. Mol. Biol. 352, 807-822 (2005).
A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1- ATPase, by Y. Q. Gao, W. Yang, and M. Karplus, Cell 123, 195-205 (2005).
Glycogen Phosphorylase Inhibitors: A Free Energy Perturbation Analysis of Glucopyranose Spirohydantoin Analogues, by G. Archontis, K. A. Watson, Q. Xie, G. Andreou, E. D. Chrysina, S. E. Zographos, N. G. Oikonomakos, L. N. Johnson, and M. Karplus, Proteins: Structure, Function & Bioinformatics 61, 984-998 (2005).
Potential Energy Surface and Nuclear dynamics of Bound MbNO, by D. R. Nutt, M. Karplus, and M. Meuwly, J. Phys. Chem. 109, 21118-21125 (2005).