Selected Publications

2019
S. Conti and M. Karplus. 2019. “Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.” PLoS computational biology, 15, 4, Pp. e1006954.
W. Hwang and M. Karplus. 2019. “Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins.” Proceedings of the National Academy of Sciences of the United States of America.
K. Nam and M. Karplus. 2019. “Insights into the origin of the high energy-conversion efficiency of F1-ATPase.” Proceedings of the National Academy of Sciences of the United States of America, 116, 32, Pp. 15924–15929.
2018
G.W. Buchko, S.V.S.R.K. Pulavarti, V. Ovchinnikov, E.A. Shaw, S.A. Rettie, P.J. Myler, M. Karplus, T. Szyperski, D. Baker, and C.D. Bahl. 2018. “Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.” Protein science : a publication of the Protein Society, 27, 9, Pp. 1611–1623.
V. Ovchinnikov, J.E. Louveau, J.P. Barton, M. Karplus, and A.K. Chakraborty. 2018. “Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies.” eLife, 7.
K. El Hage, F. H'edin, P.K. Gupta, M. Meuwly, and M. Karplus. 2018. “Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.” eLife, 7.
V. Ovchinnikov, T.A. Stone, C.M. Deber, and M. Karplus. 2018. “Structure of the EmrE Multidrug Transporter and Its Use for Inhibitor Peptide Design.” Proceedings of the National Academy of Sciences of the United States of America, 115, 34, Pp. E7932–E7941.
2017
Y. Meroz, V. Ovchinnikov, and M. Karplus. 2017. “Coexisting Origins of Subdiffusion in Internal Dynamics of Proteins.” Phys. Rev. E, 95, Pp. 062403.
Xiya Lu, Victor Ovchinnikov, Darren Demapan, Daniel Roston, and Qiang Cui. 2017. “Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.” Biochemistry, 56, 10, Pp. 1482–1497. Publisher's Version
Mason Klein, Sergei V Krivov, Anggie J Ferrer, Linjiao Luo, Aravinthan D. T. Samuel, and Martin Karplus. 2017. “Exploratory search during directed navigation in C. elegans and Drosophila larva.” Edited by Yibing Shan. eLife, 6, Pp. e30503. Publisher's VersionAbstract
Many organisms—from bacteria to nematodes to insect larvae—navigate their environments by biasing random movements. In these organisms, navigation in isotropic environments can be characterized as an essentially diffusive and undirected process. In stimulus gradients, movement decisions are biased to drive directed navigation toward favorable environments. How does directed navigation in a gradient modulate random exploration either parallel or orthogonal to the gradient? Here, we introduce methods originally used for analyzing protein folding trajectories to study the trajectories of the nematode \textitCaenorhabditis elegans and the \textitDrosophila larva in isotropic environments, as well as in thermal and chemical gradients. We find that the statistics of random exploration in any direction are little affected by directed movement along a stimulus gradient. A key constraint on the behavioral strategies of these organisms appears to be the preservation of their capacity to continuously explore their environments in all directions even while moving toward favorable conditions.
2016
X. Lu, D. Fang, S. Ito, Y. Okamoto, V. Ovchinnikov, and Q. Cui. 2016. “QM/MM free energy simulations: recent progress and challenges.” Mol. Sim., 42, Pp. 1052-1078.
V. Ovchinnikov, K. Nam, and M. Karplus. 2016. “A Simple and Accurate Method to Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.” J. Phys. Chem. B, 120, Pp. 8457-8472.
Martin Karplus. 2016. Les grands defis de la bio-informatique. TERATEC. Les Cles du futur, Pp. 64-65. Publisher's Version
2015
P. Ojeda-May, Y. Li, V. Ovchinnikov, and K. Nam. 2015. “Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase.” J. Am. Chem. Soc., 137, Pp. 12454-12457.
2014
M. Karplus. 2014. “Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel Lecture).” Angewandte Chemie (International ed. in English), 53, 38, Pp. 9992–10005.
Igor V. Kalgin, Sergei F. Chekmarev, and Martin Karplus. 2014. “First Passage Analysis of the Folding of a β-Sheet Miniprotein: Is it More Realistic Than the Standard Equilibrium Approach?” The Journal of Physical Chemistry B, 118, 16, Pp. 4287-4299. Publisher's Version
K. Nam, J. Pu, and M. Karplus. 2014. “Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism.” Proc. Natl. Acad. Sci. USA, 111, Pp. 17851-17856.
V. Ovchinnikov and M. Karplus. 2014. “Investigations of α-helix→β-sheet transition pathways in a miniprotein using the finite-temperature string method.” The Journal of chemical physics, 140, 17, Pp. 175103.
2013
G. Zheng, M. Schaefer, and M. Karplus. 2013. “Hemoglobin Bohr effects: atomic origin of the histidine residue contributions.” Biochemistry, 52, 47, Pp. 8539–55.
I.V. Kalgin, A. Caflisch, S.F. Chekmarev, and M. Karplus. 2013. “New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.” The journal of physical chemistry. B, 117, 20, Pp. 6092–105.

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