Publications

Most recent publications

(* indicates co-corresponding authors)

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect routes. Grace Kroner, Michael Wolfe, and Peter Freddolino. Journal of Bacteriology, in press. [http]

The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Elizabeth Abshire, Jennifer Chasseur, Jennifer Bohn, Paul Del Rizzo, Peter Freddolino, Aaron Goldstrohm, and Raymond Trievel. Nucleic Acids Research, 46(12):6257-6270, 2018. [html]

Cellular Adaptation Through Fitness-Directed Transcriptional Tuning. Peter L. Freddolino, Jamie Yang, Amir Roknabadi, and Saeed Tavazoie. eLife, 7:e31867, 2018.  [html]

MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Chengxin Zhang, Wei Zheng, Peter L. Freddolino, and Yang Zhang. Journal of Molecular Biology430(15):2256-2265, 2018. [html]

Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. Jennifer A. Bohn, Jamie L. Van Etten, Trista L. Schagat, Brittany M. Bowman, Richard C. McEachin, Peter L. Freddolino*, and Aaron C. Goldstrohm*. Nucleic Acids Research, 46:362-386, 2018. [html]

Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter. Paula V. Bulieris, Nausad H. Shaikh, Peter L. Freddolino, and Fadel A. Samatey. Scientific Reports, 7:15743, 2017. [html]

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. Clive Barker, Irina Meshcheryakova, Alla Kostyukova, Peter Freddolino, and Fadel Samatey. BMC Biology, 15:97, 2017. [html]

COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Chengxin Zhang, Peter L Freddolino*, and Yang Zhang*. Nucleic Acids Research, W1:W291-W299, 2017. [html]

Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes. Morteza Khabiri and Peter L. Freddolino. Journal of Physical Chemistry B, 121:5151-5161, 2017. [html]

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 and book chapters

Ab initio protein structure prediction. Jooyoung Lee, Peter L. Freddolino, and Yang Zhang. In D. J. Rigden, editor, From Protein Structure to Function with Bioinformatics. Chapter 1. Springer-London, 2017. [book website]

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]