Karplus M - Search Results

1

ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning.

Conti S, Ovchinnikov V, Karplus M. Conti S, et al. Among authors: karplus m. J Comput Chem. 2022 Sep 30;43(25):1747-1757. doi: 10.1002/jcc.26974. Epub 2022 Aug 5. J Comput Chem. 2022. PMID: 35930347

2

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

Conti S, Karplus M. Conti S, et al. Among authors: karplus m. PLoS Comput Biol. 2019 Apr 10;15(4):e1006954. doi: 10.1371/journal.pcbi.1006954. eCollection 2019 Apr. PLoS Comput Biol. 2019. PMID: 30970017 Free PMC article.

3

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

4

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

5

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

6

Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site.

Conti S, Kaczorowski KJ, Song G, Porter K, Andrabi R, Burton DR, Chakraborty AK, Karplus M. Conti S, et al. Among authors: karplus m. Proc Natl Acad Sci U S A. 2021 Mar 2;118(9):e2018338118. doi: 10.1073/pnas.2018338118. Proc Natl Acad Sci U S A. 2021. PMID: 33637649 Free PMC article.

7

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

8

A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance.

Ovchinnikov V, Karplus M. Ovchinnikov V, et al. Among authors: karplus m. Front Immunol. 2022 Mar 18;13:816634. doi: 10.3389/fimmu.2022.816634. eCollection 2022. Front Immunol. 2022. PMID: 35371013 Free PMC article.

9

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.

Conti S, Ovchinnikov V, Faris JG, Chakraborty AK, Karplus M, Sprenger KG. Conti S, et al. Among authors: karplus m. PLoS Comput Biol. 2022 Apr 20;18(4):e1009391. doi: 10.1371/journal.pcbi.1009391. eCollection 2022 Apr. PLoS Comput Biol. 2022. PMID: 35442968 Free PMC article.

10

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.

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