Follow
Luke Czapla
Title
Cited by
Cited by
Year
Sequence-dependent effects in the cyclization of short DNA
L Czapla, D Swigon, WK Olson
Journal of chemical theory and computation 2 (3), 685-695, 2006
1082006
Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding
J Park, L Czapla, RE Amaro
Journal of chemical information and modeling 53 (8), 2047-2056, 2013
482013
DNA topology confers sequence specificity to nonspecific architectural proteins
J Wei, L Czapla, MA Grosner, D Swigon, WK Olson
Proceedings of the National Academy of Sciences 111 (47), 16742-16747, 2014
452014
Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins
L Czapla, JP Peters, EM Rueter, WK Olson, LJ Maher III
Journal of molecular biology 409 (2), 278-289, 2011
442011
Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations
L Czapla, D Swigon, WK Olson
Journal of molecular biology 382 (2), 353-370, 2008
412008
How stiff is DNA?
G Zheng, L Czapla, AR Srinivasan, WK Olson
Physical Chemistry Chemical Physics 12 (6), 1399-1406, 2010
362010
Interplay of protein and DNA structure revealed in simulations of the lac operon
L Czapla, MA Grosner, D Swigon, WK Olson
PLoS One 8 (2), e56548, 2013
332013
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores
PM De Biase, CJF Solano, S Markosyan, L Czapla, SY Noskov
Journal of Chemical Theory and Computation 8 (7), 2540-2551, 2012
302012
Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore
S Markosyan, PM De Biase, L Czapla, O Samoylova, G Singh, J Cuervo, ...
Nanoscale 6 (15), 9006-9016, 2014
202014
Insights into the sequence-dependent macromolecular properties of DNA from base-pair level modeling
WK Olson, AV Colasanti, L Czapla, G Zheng
Coarse-graining of condensed phase and biomolecular systems, 205-223, 2008
182008
Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations
WK Olson, MA Grosner, L Czapla, D Swigon
Biochemical Society Transactions 41 (2), 559-564, 2013
112013
Revisiting DNA sequence-dependent deformability in high-resolution structures: effects of flanking base pairs on dinucleotide morphology and global chain configuration
RT Young, L Czapla, ZO Wefers, BM Cohen, WK Olson
Life 12 (5), 759, 2022
102022
DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi
LW Votapka, L Czapla, M Zhenirovskyy, RE Amaro
Communications in Computational Physics 13 (1), 256-268, 2013
72013
III Understanding apparent DNA flexibility enhancement by HU and HMGB proteins: experiment and simulation
L Czapla, JP Peters, EM Rueter, WK Olson, LJ Maher III
J Mol Biol 409 (2), 278-289, 2011
52011
DNA simulation benchmarks revealed with the accumulation of high-resolution structures
WK Olson, RT Young, L Czapla
Biophysical Reviews, 1-10, 2024
12024
Free energy monte carlo simulations on a distributed network
L Czapla, A Siretskiy, J Grime, MO Khan
Applied Parallel and Scientific Computing: 10th International Conference …, 2012
12012
Effect of Tetrameric Base-Pair Context on the Sequence-Dependent Configurations of DNA Minicircles
RT Young, B Cohen, L Czapla, PJ Perez, WK Olson
Biophysical Journal 116 (3), 358a-359a, 2019
2019
Molecular simulations of cytochrome P450 3A4
L Czapla, RE Amaro, M Kontoyianni
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 243, 2012
2012
Developing open-source tools to streamline computational research
LW Votapka, L Czapla, M Zhenirovskyy, O Demir, RE Amaro
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 243, 2012
2012
The Role of Architectural Proteins in Lac-Mediated DNA Looping
L Czapla, D Swigon, WK Olson
Biophysical Journal 100 (3), 71a, 2011
2011
The system can't perform the operation now. Try again later.
Articles 1–20