Template:Publications

• P. Christoph Champ and Carlos J. Camacho (2007; in press). FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Research (Web Issue) [NAR-00339-Web-B-2007.R1]
• P. Christoph Champ, Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. Microbiology, 152(3):579-583 DOI:10.1099/mic.0.28637-0 . [HubMed]
• Carlos J. Camacho, Ma H, and P. Christoph Champ (2006). Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. Proteins, 63(4):868-77 DOI:10.1002/prot.20932 . [HubMed]
• P. Christoph Champ, Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510 DOI:10.1093/nar/gkh988 . [HubMed] (The Online server of ZHunt can be found here)

Citations:

→ Bala Gupta V, Hegde, ML, Jagnnathan Rao KS (2006). Role of Protein Conformational Dynamics and DNA Integrity in Relevance to Neuronal Cell Death in Neurodegeneration. Current Alzheimer Research, 3(4):297-309(13); DOI:10.2174/156720506778249452 .

→ Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG (2006). Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations. J Human Genetics, 120(4):519-526; DOI:10.1007/s00439-006-0222-1 .

→ Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M (2006). Effect of Sequence-Directed Nucleosome Disruption on Cell-Type-Specific Repression by α2/Mcm1 in the Yeast Genome. Eukaryotic Cell, 5(11):1925-1933. DOI:10.1128/EC.00105-06

→ Kastenholz MA, Schwartz TU, Hunenberger PH (2006). The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. Biophys J, 91:2976-2990.

→ Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Mol Cell Biol, 26(7):2550-9.

→ Quyen DV, Kim KK, Kim YG (2006). Sequence-dependent kinetic behavior of protein-induced B- to Z-DNA transition. Bulletin of the Korean Chemical Society, 27(7):1071-1074.

→ Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.

→ Kwon JA, Rich A (2005). Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. Proc Natl Acad Sci USA, 102:12759-12764.

Acknowledgments:

→ Camacho CJ, Zhang C (2005). FastContact: rapid estimate of contact and binding free energies. Bioinformatics, 21(10):2534-2536; DOI:10.1093/bioinformatics/bti322 .

BibTeX

@article{champ2004dzd,
  title={{Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation}},
  author={Champ, P.C. and Maurice, S. and Vargason, J.M. and Camp, T. and Ho, P.S.},
  journal={Nucleic Acids Research},
  volume={32},
  number={22},
  pages={6501},
  year={2004},
  publisher={Oxford Univ Press}
}
@misc{champ2006gup,
  title={{Genome update: purine strand bias in 280 bacterial genomes}},
  author={Champ, P.C. and Binnewies, T.T. and Nielsen, N. and Zinman, G. and Kiil, K. and Wu, H. and Bohlin, J. and Ussery, D.W.},
  year={2006},
  publisher={Soc General Microbiol}
}

@article{camacho2006sds,
  title={{Scoring a Diverse Set of High-Quality Docked Conformations: A Metascore Based on Electrostatic and Desolvation Interactions}},
  author={Camacho, C.J. and Ma, H. and Champ, P.C.},
  journal={PROTEINS: Structure, Function, and Bioinformatics},
  volume={63},
  pages={868--877},
  year={2006}
}