Software downloads

LCVM² cgDNA publications

All LCVM² publications


Projects:

cgDNA+: a sequence-dependent rigid-base and rigid-phosphate model of DNA

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cgDNAweb: a web based viewer for the cgDNA model

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Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA

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Sequence-dependent persistence lengths of DNA

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µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

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cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA

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A sequence-dependent rigid-base model of DNA

Sequence-dependent persistence lengths of DNA

A study of DNA persistence lengths using a code cgDNAmc to run Monte Carlo simulations within the cgDNA coarse grain model. The cgDNAmc simulation code, as well as the cgDNAparamset2 used in the simulations are available for download.

• Jonathan S. Mitchell, Jaroslaw Glowacki, Alexandre E. Grandchamp, Robert S. Manning and John H. Maddocks, Sequence-dependent persistence lengths of DNA. Journal of Chemical Theory and Computation 13, 2017; doi:10.1021/acs.jctc.6b00904. (PDF of the main text and the supporting information)

Download cgDNAmc