Karplus M - Search Results

1

Coexisting origins of subdiffusion in internal dynamics of proteins.

Meroz Y, Ovchinnikov V, Karplus M. Meroz Y, et al. Among authors: karplus m. Phys Rev E. 2017 Jun;95(6-1):062403. doi: 10.1103/PhysRevE.95.062403. Epub 2017 Jun 6. Phys Rev E. 2017. PMID: 28709262

2

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. Ovchinnikov V, et al. Among authors: karplus m. J Phys Chem B. 2016 Aug 25;120(33):8457-72. doi: 10.1021/acs.jpcb.6b02139. Epub 2016 May 26. J Phys Chem B. 2016. PMID: 27135391

3

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model.

Ovchinnikov V, Conti S, Lau EY, Lightstone FC, Karplus M. Ovchinnikov V, et al. Among authors: karplus m. J Chem Theory Comput. 2020 Mar 10;16(3):1866-1881. doi: 10.1021/acs.jctc.9b01072. Epub 2020 Feb 11. J Chem Theory Comput. 2020. PMID: 32045240

4

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

Ovchinnikov V, Karplus M. Ovchinnikov V, et al. Among authors: karplus m. J Phys Chem B. 2012 Jul 26;116(29):8584-603. doi: 10.1021/jp212634z. Epub 2012 Mar 28. J Phys Chem B. 2012. PMID: 22409258 Free PMC article.

5

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

Ovchinnikov V, Cecchini M, Karplus M. Ovchinnikov V, et al. Among authors: karplus m. J Phys Chem B. 2013 Jan 24;117(3):750-62. doi: 10.1021/jp3080578. Epub 2013 Jan 10. J Phys Chem B. 2013. PMID: 23268557 Free PMC article.

6

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

Ovchinnikov V, Louveau JE, Barton JP, Karplus M, Chakraborty AK. Ovchinnikov V, et al. Among authors: karplus m. Elife. 2018 Feb 14;7:e33038. doi: 10.7554/eLife.33038. Elife. 2018. PMID: 29442996 Free PMC article.

7

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

Ovchinnikov V, Stone TA, Deber CM, Karplus M. Ovchinnikov V, et al. Among authors: 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. Proc Natl Acad Sci U S A. 2018. PMID: 30082384 Free PMC article.

8

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. Buchko GW, et al. Among authors: karplus m. Protein Sci. 2018 Sep;27(9):1611-1623. doi: 10.1002/pro.3453. Protein Sci. 2018. PMID: 30152054 Free PMC article.

9

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.

Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL. Shigdel UK, et al. Among authors: karplus m. Nat Commun. 2020 Sep 7;11(1):4437. doi: 10.1038/s41467-020-18290-2. Nat Commun. 2020. PMID: 32895378 Free PMC article.

10

Molecular Simulation of Stapled Peptides.

Ovchinnikov V, Munasinghe A, Karplus M. Ovchinnikov V, et al. Among authors: karplus m. Methods Mol Biol. 2022;2405:283-301. doi: 10.1007/978-1-0716-1855-4_14. Methods Mol Biol. 2022. PMID: 35298819

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