James J Havranek
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Explore the profile of James J Havranek including associated specialties, affiliations and a list of published articles.
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24
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2112
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Recent Articles
1.
Joyce A, Havranek J
Quant Biol
. 2023 Nov;
6(1):68-84.
PMID: 37990674
Background: Sequence-specific binding by transcription factors (TFs) plays a significant role in the selection and regulation of target genes. At the protein:DNA interface, amino acid side-chains construct a diverse physicochemical...
2.
Bodmer N, Havranek J
PLoS One
. 2018 Apr;
13(4):e0195578.
PMID: 29641557
The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development...
3.
Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq
Chang Y, Srivastava Y, Hu C, Joyce A, Yang X, Zuo Z, et al.
Nucleic Acids Res
. 2016 Dec;
45(2):832-845.
PMID: 27915232
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious...
4.
Zhang C, Myers C, Qi Z, Mitra R, Corbo J, Havranek J
Nucleic Acids Res
. 2015 Sep;
43(18):9076-85.
PMID: 26365240
Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a...
5.
Sasaki Y, Margolin Z, Borgo B, Havranek J, Milbrandt J
J Biol Chem
. 2015 May;
290(28):17228-38.
PMID: 26018082
Leber congenital amaurosis 9 (LCA9) is an autosomal recessive retinal degeneration condition caused by mutations in the NAD(+) biosynthetic enzyme NMNAT1. This condition leads to early blindness but no other...
6.
Joyce A, Zhang C, Bradley P, Havranek J
Brief Funct Genomics
. 2014 Nov;
14(1):39-49.
PMID: 25414269
Protein:DNA interactions are essential to a range of processes that maintain and express the information encoded in the genome. Structural modeling is an approach that aims to understand these interactions...
7.
Borgo B, Havranek J
Protein Sci
. 2014 Jan;
23(3):312-20.
PMID: 24407908
Computational protein design relies on several approximations, including the use of fixed backbones and rotamers, to reduce protein design to a computationally tractable problem. However, allowing backbone and off-rotamer flexibility...
8.
Lyskov S, Chou F, Conchuir S, Der B, Drew K, Kuroda D, et al.
PLoS One
. 2013 May;
8(5):e63906.
PMID: 23717507
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of...
9.
Leaver-Fay A, OMeara M, Tyka M, Jacak R, Song Y, Kellogg E, et al.
Methods Enzymol
. 2013 Feb;
523:109-43.
PMID: 23422428
Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these...
10.
Tang Y, Gao R, Havranek J, Groisman E, Stock A, Marshall G
Chem Biol Drug Des
. 2012 Feb;
79(6):1007-17.
PMID: 22339993
Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. A typical TCST system consists...