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Items: 13

1.

pydca v1.0: A Comprehensive Software for Direct Coupling Analysis of RNA and Protein Sequences.

Zerihun MB, Pucci F, Peter EK, Schug A.

Bioinformatics. 2019 Nov 28. pii: btz892. doi: 10.1093/bioinformatics/btz892. [Epub ahead of print]

PMID:
31778142
2.

A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients.

Ek P, Böttiger B, Dahlman D, Hansen KB, Nyman M, Nilsson AC.

Infect Dis (Lond). 2019 Apr;51(4):241-248. doi: 10.1080/23744235.2018.1546055. Epub 2019 Feb 14.

PMID:
30760088
3.

A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.

Peter EK, Černý J.

Int J Mol Sci. 2019 Jan 16;20(2). pii: E370. doi: 10.3390/ijms20020370.

4.

Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank.

Peter EK, Cerny J.

Int J Mol Sci. 2018 Oct 30;19(11). pii: E3405. doi: 10.3390/ijms19113405.

5.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

Peter EK.

J Chem Phys. 2017 Dec 7;147(21):214902. doi: 10.1063/1.5000930.

PMID:
29221375
6.

An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation.

Peter EK, Shea JE.

Phys Chem Chem Phys. 2017 Jul 5;19(26):17373-17382. doi: 10.1039/c7cp03035e.

PMID:
28650060
7.

A canonical replica exchange molecular dynamics implementation with normal pressure in each replica.

Peter EK, Pivkin IV, Shea JE.

J Chem Phys. 2016 Jul 28;145(4):044903. doi: 10.1063/1.4958325.

PMID:
27475393
8.

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent.

Peter EK, Shea JE, Pivkin IV.

Phys Chem Chem Phys. 2016 May 14;18(18):13052-65. doi: 10.1039/c5cp06867c. Epub 2016 Apr 25.

PMID:
27111190
9.

A polarizable coarse-grained protein model for dissipative particle dynamics.

Peter EK, Lykov K, Pivkin IV.

Phys Chem Chem Phys. 2015 Oct 7;17(37):24452-61. doi: 10.1039/c5cp03479e. Epub 2015 Sep 4.

PMID:
26339692
10.

A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides.

Peter EK, Pivkin IV, Shea JE.

J Chem Phys. 2015 Apr 14;142(14):144903. doi: 10.1063/1.4915919.

PMID:
25877593
11.

How water layers on graphene affect folding and adsorption of TrpZip2.

Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE.

J Chem Phys. 2014 Dec 14;141(22):22D511. doi: 10.1063/1.4896984.

PMID:
25494782
12.

A polarizable coarse-grained water model for dissipative particle dynamics.

Peter EK, Pivkin IV.

J Chem Phys. 2014 Oct 28;141(16):164506. doi: 10.1063/1.4899317.

PMID:
25362324
13.

A hybrid MD-kMC algorithm for folding proteins in explicit solvent.

Peter EK, Shea JE.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6430-40. doi: 10.1039/c3cp55251a. Epub 2014 Feb 5.

PMID:
24499973

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