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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins.

Hwang W, Karplus M.

Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):19777-19785. doi: 10.1073/pnas.1818589116. Epub 2019 Sep 10.


Insights into the origin of the high energy-conversion efficiency of F1-ATPase.

Nam K, Karplus M.

Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):15924-15929. doi: 10.1073/pnas.1906816116. Epub 2019 Jul 24.


Lateral variation of the Main Himalayan Thrust controls the rupture length of the 2015 Gorkha earthquake in Nepal.

Bai L, Klemperer SL, Mori J, Karplus MS, Ding L, Liu H, Li G, Song B, Dhakal S.

Sci Adv. 2019 Jun 26;5(6):eaav0723. doi: 10.1126/sciadv.aav0723. eCollection 2019 Jun.


Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M.

Elife. 2019 Jun 20;8. pii: e45318. doi: 10.7554/eLife.45318.


Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.

Conti S, Karplus M.

PLoS Comput Biol. 2019 Apr 10;15(4):e1006954. doi: 10.1371/journal.pcbi.1006954. eCollection 2019 Apr.


Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.

Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD.

Protein Sci. 2018 Sep;27(9):1611-1623. doi: 10.1002/pro.3453.


Structure of the EmrE multidrug transporter and its use for inhibitor peptide design.

Ovchinnikov V, Stone TA, Deber CM, Karplus M.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):E7932-E7941. doi: 10.1073/pnas.1802177115. Epub 2018 Aug 6.


Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.

El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M.

Elife. 2018 Jul 12;7. pii: e35560. doi: 10.7554/eLife.35560.


Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies.

Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK.

Elife. 2018 Feb 14;7. pii: e33038. doi: 10.7554/eLife.33038.


Kinesin motility is driven by subdomain dynamics.

Hwang W, Lang MJ, Karplus M.

Elife. 2017 Nov 7;6. pii: e28948. doi: 10.7554/eLife.28948.


Exploratory search during directed navigation in C. elegans and Drosophila larva.

Klein M, Krivov SV, Ferrer AJ, Luo L, Samuel AD, Karplus M.

Elife. 2017 Oct 30;6. pii: e30503. doi: 10.7554/eLife.30503.


Coexisting origins of subdiffusion in internal dynamics of proteins.

Meroz Y, Ovchinnikov V, Karplus M.

Phys Rev E. 2017 Jun;95(6-1):062403. doi: 10.1103/PhysRevE.95.062403. Epub 2017 Jun 6.


A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

Ovchinnikov V, Nam K, Karplus M.

J Phys Chem B. 2016 Aug 25;120(33):8457-72. doi: 10.1021/acs.jpcb.6b02139. Epub 2016 May 26.


Do Prenatal Corticosteroids Affect Brain Maturation of the Premature Infant? An Electroencephalography Study.

Shany E, Berger I, Goldberg O, Karplus M, Gilat S, Benzaquen O, Yogev H, Shalev R.

Clin EEG Neurosci. 2017 Mar;48(2):79-87. doi: 10.1177/1550059416643202. Epub 2016 Jul 10.


Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism.

Nam K, Pu J, Karplus M.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17851-6. doi: 10.1073/pnas.1419486111. Epub 2014 Dec 1.


Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel Lecture).

Karplus M.

Angew Chem Int Ed Engl. 2014 Sep 15;53(38):9992-10005. doi: 10.1002/anie.201403924. Epub 2014 Jul 27. No abstract available.


Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.

Ovchinnikov V, Karplus M.

J Chem Phys. 2014 May 7;140(17):175103. doi: 10.1063/1.4871685.


First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach?

Kalgin IV, Chekmarev SF, Karplus M.

J Phys Chem B. 2014 Apr 24;118(16):4287-99. doi: 10.1021/jp412729r. Epub 2014 Apr 9.


Enhanced chemical synthesis at soft interfaces: a universal reaction-adsorption mechanism in microcompartments.

Fallah-Araghi A, Meguellati K, Baret JC, El Harrak A, Mangeat T, Karplus M, Ladame S, Marques CM, Griffiths AD.

Phys Rev Lett. 2014 Jan 17;112(2):028301. Epub 2014 Jan 13.


Hemoglobin Bohr effects: atomic origin of the histidine residue contributions.

Zheng G, Schaefer M, Karplus M.

Biochemistry. 2013 Nov 26;52(47):8539-55. doi: 10.1021/bi401126z. Epub 2013 Nov 13.


A gating mechanism of pentameric ligand-gated ion channels.

Calimet N, Simoes M, Changeux JP, Karplus M, Taly A, Cecchini M.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):E3987-96. doi: 10.1073/pnas.1313785110. Epub 2013 Sep 16. Review.


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.

Kalgin IV, Caflisch A, Chekmarev SF, Karplus M.

J Phys Chem B. 2013 May 23;117(20):6092-105. doi: 10.1021/jp401742y. Epub 2013 May 15.


A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

Ovchinnikov V, Cecchini M, Karplus M.

J Phys Chem B. 2013 Jan 24;117(3):750-62. doi: 10.1021/jp3080578. Epub 2013 Jan 10.


Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors.

Karthikeyan G, Zambaldo C, Barluenga S, Zoete V, Karplus M, Winssinger N.

Chemistry. 2012 Jul 16;18(29):8978-86. doi: 10.1002/chem.201200546. Epub 2012 Jun 13.


Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1.

Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL.

J Biol Chem. 2012 Jul 20;287(30):24916-28. doi: 10.1074/jbc.M111.316497. Epub 2012 Apr 16.


Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.

Ovchinnikov V, Karplus M.

J Phys Chem B. 2012 Jul 26;116(29):8584-603. doi: 10.1021/jp212634z. Epub 2012 Mar 28.


Strandwise translocation of a DNA glycosylase on undamaged DNA.

Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL.

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1086-91. doi: 10.1073/pnas.1111237108. Epub 2012 Jan 4.


A conformational transition in the myosin VI converter contributes to the variable step size.

Ovchinnikov V, Cecchini M, Vanden-Eijnden E, Karplus M.

Biophys J. 2011 Nov 16;101(10):2436-44. doi: 10.1016/j.bpj.2011.09.044. Epub 2011 Nov 15.


Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

Zheng G, Niklasson AM, Karplus M.

J Chem Phys. 2011 Jul 28;135(4):044122. doi: 10.1063/1.3605303.


Behind the folding funnel diagram.

Karplus M.

Nat Chem Biol. 2011 Jun 17;7(7):401-4. doi: 10.1038/nchembio.565. Erratum in: Nat Chem Biol. 2011 Sep;7(9):648.


Determining the conformational change that accompanies donor-acceptor distance fluctuations: an umbrella sampling analysis.

Luo G, Karplus M.

J Phys Chem B. 2011 Jun 23;115(24):7991-5. doi: 10.1021/jp201998c. Epub 2011 May 27.


Unsuspected pathway of the allosteric transition in hemoglobin.

Fischer S, Olsen KW, Nam K, Karplus M.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5608-13. doi: 10.1073/pnas.1011995108. Epub 2011 Mar 17.


Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

Ovchinnikov V, Karplus M, Vanden-Eijnden E.

J Chem Phys. 2011 Feb 28;134(8):085103. doi: 10.1063/1.3544209.


Protein dynamics investigated by inherent structure analysis.

Rao F, Karplus M.

Proc Natl Acad Sci U S A. 2010 May 18;107(20):9152-7. doi: 10.1073/pnas.0915087107. Epub 2010 Apr 30.


Role of conformation transitions in adenylate kinase.

Karplus M.

Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):E71; author reply E72. doi: 10.1073/pnas.1002180107. No abstract available.


Pi release from myosin: a simulation analysis of possible pathways.

Cecchini M, Alexeev Y, Karplus M.

Structure. 2010 Mar 14;18(4):458-70. doi: 10.1016/j.str.2010.01.014.


The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.

Golosov AA, Warren JJ, Beese LS, Karplus M.

Structure. 2010 Jan 13;18(1):83-93. doi: 10.1016/j.str.2009.10.014.


Dynamical aspects of molecular recognition.

Karplus M.

J Mol Recognit. 2010 Mar-Apr;23(2):102-4. doi: 10.1002/jmr.1018. No abstract available.


PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis.

Grinthal A, Adamovic I, Weiner B, Karplus M, Kleckner N.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2467-72. doi: 10.1073/pnas.0914073107. Epub 2010 Jan 25.


Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.

Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL.

Nature. 2009 Dec 10;462(7274):762-6. doi: 10.1038/nature08561.


Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism.

Nam K, Verdine GL, Karplus M.

J Am Chem Soc. 2009 Dec 30;131(51):18208-9. doi: 10.1021/ja907544b.


Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.

Qi Y, Spong MC, Nam K, Karplus M, Verdine GL.

J Biol Chem. 2010 Jan 8;285(2):1468-78. doi: 10.1074/jbc.M109.069799. Epub 2009 Nov 4.


Mechanical coupling in myosin V: a simulation study.

Ovchinnikov V, Trout BL, Karplus M.

J Mol Biol. 2010 Jan 29;395(4):815-33. doi: 10.1016/j.jmb.2009.10.029. Epub 2009 Oct 21.


Folding of a SH3 domain: standard and "hydrodynamic" analyses.

Kalgin IV, Karplus M, Chekmarev SF.

J Phys Chem B. 2009 Sep 24;113(38):12759-72. doi: 10.1021/jp903325z.


Segmented transition pathway of the signaling protein nitrogen regulatory protein C.

Lei M, Velos J, Gardino A, Kivenson A, Karplus M, Kern D.

J Mol Biol. 2009 Sep 25;392(3):823-36. doi: 10.1016/j.jmb.2009.06.065. Epub 2009 Jul 1.


Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

Cecchini M, Krivov SV, Spichty M, Karplus M.

J Phys Chem B. 2009 Jul 23;113(29):9728-40. doi: 10.1021/jp9020646. Erratum in: J Phys Chem B. 2010 May 20;114(19):6763.


The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.

Spichty M, Taly A, Hagn F, Kessler H, Barluenga S, Winssinger N, Karplus M.

Biophys Chem. 2009 Aug;143(3):111-23. doi: 10.1016/j.bpc.2009.04.003. Epub 2009 Apr 15.


CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.

J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. Review.


Gaussian-mixture umbrella sampling.

Maragakis P, van der Vaart A, Karplus M.

J Phys Chem B. 2009 Apr 9;113(14):4664-73. doi: 10.1021/jp808381s.


Kinesin's cover-neck bundle folds forward to generate force.

Khalil AS, Appleyard DC, Labno AK, Georges A, Karplus M, Belcher AM, Hwang W, Lang MJ.

Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19247-52. doi: 10.1073/pnas.0805147105. Epub 2008 Dec 1.

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