Publications

Most recent publications

QwikMD—Integrative Molecular Dynamics Toolkit for Novices and Experts. João V Ribeiro, Rafael C Bernardi, Till Rudack, John E Stone, James C Phillips, Peter L Freddolino, and Klaus Schulten. Scientific Reports, 6: 26536, 2016. [html]

Interfacial activation of Candida antarctica lipase B: combined evidence from experiment and simulation. Themistoklis Zisis, Peter L Freddolino, Petri Turunen, Muriel CF van Teeseling, Alan E Rowan, and Kerstin G Blank. Biochemistry, 54:5969-5979, 2015. [html]

Revealing the genetic basis of natural bacterial phenotypic divergence. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. Journal of Bacteriology, 196:825-839, 2014. [html]

Bacterial Adaptation through Loss of Function. Alison K. Hottes, Peter L. Freddolino, Anupama Khare, Zachary N. Donnell, Julia C. Liu, and Saeed Tavazoie. PLoS Genetics, 9(7): e1003617, 2013. [html]

Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Peter L. Freddolino, Kevin H. Gardner, and Klaus Schulten. Photochemical and Photobiological Sciences, 12:1158-1170, 2013. [html]

The Dawn of Virtual Cell Biology. Peter L. Freddolino and Saeed Tavazoie. Cell, 150:248-250, 2012. [html]

Most representative publications

Revealing the genetic basis of natural bacterial phenotypic divergence. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. Journal of Bacteriology, 196:825-839, 2014. [html]

Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site. Sang-Hun Song, Peter L. Freddolino, Abigail I. Nash, Elizabeth C. Carroll, Klaus Schulten, Kevin H. Gardner, and Delmar S. Larsen. Biochemistry, 50:2411-2423, 2011. [html]

Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2338-2347, 2009. [html]

Force field bias in protein folding simulations. Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten. Biophysical Journal, 96:3772-3780, 2009. [html]

Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Structure, 14:437-449, 2006. [html]

Key reviews

Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior. Peter L. Freddolino and Saeed Tavazoie. Annual Review of Cell and Developmental Biology, 28:363-384, 2012. [html]

Challenges in protein-folding simulations. Peter L. Freddolino, Christopher B Harrison, Yanxin Liu, Klaus Schulten. Nature Physics, 6:751-758, 2010. [html]

Application of residue-based and shape-based coarse graining to biomolecular simulations. Peter L. Freddolino, Anton Arkhipov, Amy Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008. [book website]