• Jeffrey K Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L Hayes, José N Onuchic, and Paul C Whitford. Smog 2: a versatile software package for generating structure-based models. PLoS computational biology, 12(3):e1004794, 2016.

  • Cecilia Clementi, Hugh Nymeyer, and José Nelson Onuchic. Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins. Journal of molecular biology, 298(5):937–953, 2000.

  • Paul C Whitford, Jeffrey K Noel, Shachi Gosavi, Alexander Schug, Kevin Y Sanbonmatsu, and José N Onuchic. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins: Structure, Function, and Bioinformatics, 75(2):430–441, 2009.

  • Jeffrey K Noel, Paul C Whitford, and José N Onuchic. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. The Journal of Physical Chemistry B, 116(29):8692–8702, 2012.

  • Heiko Lammert, Alexander Schug, and José N Onuchic. Robustness and generalization of structure-based models for protein folding and function. Proteins: Structure, Function, and Bioinformatics, 77(4):881–891, 2009.

  • Jeffrey K Noel and José N Onuchic. The many faces of structure-based potentials: from protein folding landscapes to structural characterization of complex biomolecules. In Computational modeling of biological systems, pages 31–54. Springer, 2012.

  • Mariana Levi, Prasad Bandarkar, Huan Yang, Ailun Wang, Udayan Mohanty, Jeffrey K Noel, and Paul C Whitford. Using smog 2 to simulate complex biomolecular assemblies. In Biomolecular Simulations, pages 129–151. Springer, 2019.

  • Antonio B Oliveira Jr, Vinicius G Contessoto, Matheus F Mello, and Jose N Onuchic. A scalable computational approach for simulating complexes of multiple chromosomes. Journal of Molecular Biology, 433(6):166700, 2020.