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.