John H Maddocks
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Explore the profile of John H Maddocks including associated specialties, affiliations and a list of published articles.
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Articles
26
Citations
750
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Recent Articles
1.
Maddocks J, Dans P, Cheatham 3rd T, Harris S, Laughton C, Orozco M, et al.
Biophys Rev
. 2024 Aug;
16(3):259-262.
PMID: 39099838
This editorial for Volume 16, Issue 3 of highlights the three-dimensional structural and dynamic information encoded in DNA sequences and introduces the topics covered in this special issue of the...
2.
Olson W, Maddocks J, Dans P, Cheatham 3rd T, Harris S, Laughton C, et al.
Biophys Rev
. 2024 Jan;
15(6):1901-1902.
PMID: 38192348
No abstract available.
3.
Sharma R, Patelli A, De Bruin L, Maddocks J
J Mol Biol
. 2023 Jun;
435(14):167978.
PMID: 37356908
The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly...
4.
da Rosa G, Grille L, Calzada V, Ahmad K, Arcon J, Battistini F, et al.
Biophys Rev
. 2022 Jan;
13(6):995-1005.
PMID: 35059023
The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was...
5.
Grandgeorge P, Baek C, Singh H, Johanns P, Sano T, Flynn A, et al.
Proc Natl Acad Sci U S A
. 2021 Apr;
118(15).
PMID: 33876761
Networks of flexible filaments often involve regions of tight contact. Predictively understanding the equilibrium configurations of these systems is challenging due to intricate couplings between topology, geometry, large nonlinear deformations,...
6.
Dans P, Balaceanu A, Pasi M, Patelli A, Petkeviciute D, Walther J, et al.
Nucleic Acids Res
. 2019 Oct;
47(21):11090-11102.
PMID: 31624840
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine...
7.
De Bruin L, Maddocks J
Nucleic Acids Res
. 2018 Jun;
46(W1):W5-W10.
PMID: 29905876
The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to...
8.
Pasi M, Zakrzewska K, Maddocks J, Lavery R
Nucleic Acids Res
. 2017 Feb;
45(7):4269-4277.
PMID: 28180333
We propose a method for analyzing the magnitude and direction of curvature within nucleic acids, based on the curvilinear helical axis calculated by Curves+. The method is applied to analyzing...
9.
Mitchell J, Glowacki J, Grandchamp A, Manning R, Maddocks J
J Chem Theory Comput
. 2016 Dec;
13(4):1539-1555.
PMID: 28029797
A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of l = 53.5 nm in the...
10.
Pasi M, Maddocks J, Lavery R
Nucleic Acids Res
. 2015 Feb;
43(4):2412-23.
PMID: 25662221
Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact...