cgDNA group publications:
- Rahul Sharma, Alessandro S. Patelli, Lennart De Bruin, John H. Maddocks, cgNA+web : A Visual Interface to the cgNA+ Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids , EPFL 2023
- Th. Zwahlen, PhD thesis #8784, EPFL 2023
- R. Sharma, PhD thesis #9792, EPFL 2023
- O. Gonzalez, M. Pasi, D. Petkevičiūtė, J. Glowacki, J.H. Maddocks, Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA, Multiscale Model. Simul. 15 (3), 2017; doi:10.1137/16M1086091.
- J.S. Mitchell, J. Glowacki, A.E. Grandchamp, R.S. Manning and J.H. Maddocks, Sequence-dependent persistence lengths of DNA. Journal of Chemical Theory and Computation 13, 2017; doi:10.1021/acs.jctc.6b00904.
- J. Glowacki, PhD thesis #7062, EPFL 2016.
- A. E. Grandchamp, PhD thesis #6977, EPFL 2016.
- M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, P.D. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Perez, D. Petkeviciute, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery. µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research 2014; doi: 10.1093/nar/gku855.
- D. Petkevičiūtė, M. Pasi, O. Gonzalez and J.H. Maddocks. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA. Nucleic Acids Research 2014; doi: 10.1093/nar/gku825.
- O. Gonzalez, D. Petkevičiūtė, and J.H. Maddocks. A sequence-dependent rigid-base model of DNA. J. Chem. Phys. 138 (5), 2013; doi: 10.1063/1.4789411.
- D. Petkevičiūtė, PhD thesis #5520, EPFL 2012.