Peter L. Freddolino, Ph.D. - Publications

Affiliations: 
2009 University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
theoretical biophysics

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription. 1-37. PMID 34499567 DOI: 10.1080/21541264.2021.1973865  1
2021 Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S. Dynamic landscape of protein occupancy across the Escherichia coli chromosome. Plos Biology. 19: e3001306. PMID 34170902 DOI: 10.1371/journal.pbio.3001306  1
2021 Ziegler CA, Freddolino PL. The leucine-responsive regulatory proteins/feast-famine regulatory proteins: an ancient and complex class of transcriptional regulators in bacteria and archaea. Critical Reviews in Biochemistry and Molecular Biology. 56: 373-400. PMID 34151666 DOI: 10.1080/10409238.2021.1925215  0.01
2021 Platt JL, de Mattos Barbosa MG, Huynh D, Lefferts AR, Katta J, Kharas C, Freddolino PL, Bassis CM, Wobus CE, Geha R, Bram RJ, Nunez G, Kamada N, Cascalho M. TNFRSF13B polymorphisms counteract microbial adaptation to natural IgA. Jci Insight. PMID 34111031 DOI: 10.1172/jci.insight.148208  0.01
2021 Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of Proteome Research. PMID 33393786 DOI: 10.1021/acs.jproteome.0c00359  1
2020 Khabiri M, Freddolino PL. Correction to "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes". The Journal of Physical Chemistry. B. 124: 11311. PMID 33236911 DOI: 10.1021/acs.jpcb.0c10359  1
2020 Vaziri A, Khabiri M, Genaw BT, May CE, Freddolino PL, Dus M. Persistent epigenetic reprogramming of sweet taste by diet. Science Advances. 6. PMID 33177090 DOI: 10.1126/sciadv.abc8492  1
2020 Abshire ET, Hughes KL, Diao R, Pearce S, Gopalakrishna S, Trievel RC, Rorbach J, Freddolino PL, Goldstrohm AC. Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. The Journal of Biological Chemistry. PMID 32839274 DOI: 10.1074/Jbc.Ra120.012618  1
2020 Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL. Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis. Rna (New York, N.Y.). PMID 32753408 DOI: 10.1261/Rna.077362.120  1
2020 Zamora M, Ziegler CA, Freddolino PL, Wolfe AJ. A Thermosensitive, Phase-Variable Epigenetic Switch: Revisited. Microbiology and Molecular Biology Reviews : Mmbr. 84. PMID 32727743 DOI: 10.1128/Mmbr.00030-17  0.01
2020 Wei X, Zhang C, Freddolino PL, Zhang Y. Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinformatics (Oxford, England). PMID 32470107 DOI: 10.1093/bioinformatics/btaa548  1
2020 Walker DM, Freddolino PL, Harshey RM. A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition. Cell. PMID 32059782 DOI: 10.1016/J.Cell.2020.01.031  0.01
2020 Barnier C, Piersimoni L, Price J, Plasencia M, Chapman MR, Andrews PC, Freddolino PL. A Unified Workflow to Identify Quaternary Structures and Changes in Protein-protein Interactions from Crosslinking-based Mass Spectrometry Biophysical Journal. 118: 357a. DOI: 10.1016/J.Bpj.2019.11.2057  0.01
2019 Arvola RM, Chang CT, Buytendorp JP, Levdansky Y, Valkov E, Freddolino PL, Goldstrohm AC. Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs. Nucleic Acids Research. PMID 31863588 DOI: 10.1093/Nar/Gkz1187  1
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Freddolino PL, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  1
2019 Wilinski D, Winzeler J, Duren W, Persons JL, Holme KJ, Mosquera J, Khabiri M, Kinchen JM, Freddolino PL, Karnovsky A, Dus M. Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. Nature Communications. 10: 4052. PMID 31492856 DOI: 10.1038/S41467-019-11933-Z  1
2019 Sjulstok E, Solov'yov IA, Freddolino PL. Applications of molecular modeling to flavoproteins: Insights and challenges. Methods in Enzymology. 620: 277-314. PMID 31072491 DOI: 10.1016/Bs.Mie.2019.03.014  0.08
2019 May CE, Vaziri A, Lin YQ, Grushko O, Khabiri M, Wang QP, Holme KJ, Pletcher SD, Freddolino PL, Neely GG, Dus M. High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster. Cell Reports. 27: 1675-1685.e7. PMID 31067455 DOI: 10.1016/J.Celrep.2019.04.027  1
2019 Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Molecular Cell. PMID 30975459 DOI: 10.1016/J.Molcel.2019.03.014  1
2019 Scholz SA, Diao R, Wolfe MB, Fivenson EM, Lin XN, Freddolino PL. High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription. Cell Systems. PMID 30904377 DOI: 10.1016/J.Cels.2019.02.004  1
2018 Wolfe MB, Goldstrohm AC, Freddolino PL. Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods (San Diego, Calif.). PMID 30529548 DOI: 10.1016/J.Ymeth.2018.12.001  1
2018 Kroner GM, Wolfe MB, Freddolino PL. Lrp regulates one-third of the genome via direct, cooperative, and indirect routes. Journal of Bacteriology. PMID 30420454 DOI: 10.1128/Jb.00411-18  1
2018 T Abshire E, Chasseur J, Bohn JA, Del Rizzo PA, Freddolino PL, Goldstrohm AC, Trievel RC. The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Nucleic Acids Research. PMID 29860338 DOI: 10.1093/Nar/Gky412  1
2018 Khabiri M, Freddolino PL. Expression of Concern for "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes". The Journal of Physical Chemistry. B. PMID 29741907 DOI: 10.1021/Acs.Jpcb.8B04187  1
2018 Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. Elife. 7. PMID 29620524 DOI: 10.7554/Elife.31867  1
2018 Zhang C, Zheng W, Freddolino PL, Zhang Y. MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology. PMID 29534977 DOI: 10.1016/J.Jmb.2018.03.004  1
2018 Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Author response: Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry Elife. DOI: 10.7554/Elife.31867.052  1
2017 Bohn JA, Van Etten JL, Schagat TL, Bowman BM, McEachin RC, Freddolino PL, Goldstrohm AC. Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. Nucleic Acids Research. PMID 29165587 DOI: 10.1093/Nar/Gkx1120  1
2017 Bulieris PV, Shaikh NH, Freddolino PL, Samatey FA. Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter. Scientific Reports. 7: 15743. PMID 29147015 DOI: 10.1038/S41598-017-15837-0  1
2017 Barker CS, Meshcheryakova IV, Kostyukova AS, Freddolino PL, Samatey FA. An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. Bmc Biology. 15: 97. PMID 29078764 DOI: 10.1186/S12915-017-0438-7  1
2017 Zhang C, Freddolino PL, Zhang Y. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research. PMID 28472402 DOI: 10.1093/Nar/Gkx366  1
2017 Khabiri M, Freddolino PL. Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes. The Journal of Physical Chemistry. B. PMID 28471184 DOI: 10.1021/Acs.Jpcb.6B12450  1
2017 Freddolino PL, Goss TJ, Kroner GM, Scholz S, Lin X. Effects of Large Scale Protein Occupancy on E. Coli Genome Structure and Gene Expression Biophysical Journal. 112: 573a. DOI: 10.1016/J.Bpj.2016.11.3085  0.01
2016 Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K. QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts. Scientific Reports. 6: 26536. PMID 27216779 DOI: 10.1038/Srep26536  1
2015 Zisis T, Freddolino PL, Turunen P, van Teeseling MC, Rowan AE, Blank KG. Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation. Biochemistry. 54: 5969-79. PMID 26346632 DOI: 10.1021/Acs.Biochem.5B00586  0.01
2014 Freddolino PL, Goodarzi H, Tavazoie S. Revealing the genetic basis of natural bacterial phenotypic divergence. Journal of Bacteriology. 196: 825-39. PMID 24317396 DOI: 10.1128/Jb.01039-13  1
2013 Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S. Bacterial adaptation through loss of function. Plos Genetics. 9: e1003617. PMID 23874220 DOI: 10.1371/Journal.Pgen.1003617  1
2013 Freddolino PL, Gardner KH, Schulten K. Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 12: 1158-70. PMID 23407663 DOI: 10.1039/C3Pp25400C  1
2013 Rajan A, Freddolino PL, Schulten K. PCA and nMDS embedded representation of trajectory 1 applied to dihedral angle space. Plos One. DOI: 10.1371/Journal.Pone.0009890.G003  1
2013 Freddolino P, Tavazoie S. Genome-Wide Measurement of Bacterial Transcriptional Regulatory States Biophysical Journal. 104: 328a. DOI: 10.1016/J.Bpj.2012.11.1820  0.01
2012 Freddolino PL, Tavazoie S. The dawn of virtual cell biology. Cell. 150: 248-50. PMID 22817888 DOI: 10.1016/J.Cell.2012.07.001  1
2012 Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K. Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters. 3: 1117-1123. PMID 22737279 DOI: 10.1021/Jz300017C  1
2012 Freddolino PL, Goodarzi H, Tavazoie S. Fitness landscape transformation through a single amino acid change in the rho terminator. Plos Genetics. 8: e1002744. PMID 22693458 DOI: 10.1371/Journal.Pgen.1002744  1
2012 Freddolino PL, Tavazoie S. Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior. Annual Review of Cell and Developmental Biology. 28: 363-84. PMID 22559263 DOI: 10.1146/Annurev-Cellbio-092910-154129  1
2012 Freddolino PL, Amini S, Tavazoie S. Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. Journal of Bacteriology. 194: 303-6. PMID 22081388 DOI: 10.1128/Jb.06087-11  1
2012 Liu Y, Strumpfer J, Freddolino PL, Gruebele M, Schulten K. Folding Thermodynamics and Kinetics of Lambda-Repressor from All-Atom Molecular Dynamics Simulations Biophysical Journal. 102: 4-7. DOI: 10.1016/J.Bpj.2011.11.2506  1
2011 Schreiner E, Trabuco LG, Freddolino PL, Schulten K. Stereochemical errors and their implications for molecular dynamics simulations. Bmc Bioinformatics. 12: 190. PMID 21605430 DOI: 10.1186/1471-2105-12-190  1
2011 Song SH, Freddolino PL, Nash AI, Carroll EC, Schulten K, Gardner KH, Larsen DS. Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site. Biochemistry. 50: 2411-23. PMID 21323358 DOI: 10.1021/Bi200198X  1
2010 Freddolino PL, Harrison CB, Liu Y, Schulten K. Challenges in protein folding simulations: Timescale, representation, and analysis. Nature Physics. 6: 751-758. PMID 21297873 DOI: 10.1038/Nphys1713  1
2010 Cerutti DS, Freddolino PL, Duke RE, Case DA. Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models. The Journal of Physical Chemistry. B. 114: 12811-24. PMID 20860388 DOI: 10.1021/Jp105813J  1
2010 Rajan A, Freddolino PL, Schulten K. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. Plos One. 5: e9890. PMID 20419160 DOI: 10.1371/Journal.Pone.0009890  1
2009 Freddolino PL, Schulten K. Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal. 97: 2338-47. PMID 19843466 DOI: 10.1016/J.Bpj.2009.08.012  1
2009 Freddolino PL, Park S, Roux B, Schulten K. Force field bias in protein folding simulations. Biophysical Journal. 96: 3772-80. PMID 19413983 DOI: 10.1016/J.Bpj.2009.02.033  1
2009 Freddolino PL, Liu F, Park S, Gruebele M, Schulten K. Microsecond Explicit Solvent Molecular Dynamics Simulations of Protein Folding Biophysical Journal. 96: 590a. DOI: 10.1016/J.Bpj.2008.12.3090  0.04
2008 Cerutti DS, Duke R, Freddolino PL, Fan H, Lybrand TP. Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics. Journal of Chemical Theory and Computation. 4: 1669-1680. PMID 19180249 DOI: 10.1021/Ct8002173  1
2008 Yao Y, Harrison CB, Freddolino PL, Schulten K, Mayer ML. Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. The Embo Journal. 27: 2158-70. PMID 18636091 DOI: 10.1038/Emboj.2008.140  1
2008 Freddolino PL, Liu F, Gruebele M, Schulten K. Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal. 94: L75-7. PMID 18339748 DOI: 10.1529/Biophysj.108.131565  1
2008 Freddolino PL, Dittrich M, Schulten K. Erratum: Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins (Biophysical Journal (2006) 91 (3630-3639)) Biophysical Journal. 94. DOI: 10.1529/Biophysj.108.0900176  1
2008 Shih AY, Freddolino PL, Arkhipov A, Sligar SG, Schulten K. Chapter 11 Molecular Modeling of the Structural Properties and Formation of High-Density Lipoprotein Particles Current Topics in Membranes. 60: 313-342. DOI: 10.1016/S1063-5823(08)00011-2  1
2007 Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry. 28: 2618-40. PMID 17894371 DOI: 10.1002/Jcc.20829  1
2007 Shih AY, Arkhipov A, Freddolino PL, Sligar SG, Schulten K. Assembly of lipids and proteins into lipoprotein particles. The Journal of Physical Chemistry. B. 111: 11095-104. PMID 17696388 DOI: 10.1021/Jp072320B  1
2007 Shih AY, Freddolino PL, Sligar SG, Schulten K. Disassembly of nanodiscs with cholate. Nano Letters. 7: 1692-6. PMID 17503871 DOI: 10.1021/Nl0706906  1
2007 Shih AY, Freddolino PL, Arkhipov A, Schulten K. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Journal of Structural Biology. 157: 579-92. PMID 17070069 DOI: 10.1016/J.Jsb.2006.08.006  1
2006 Arkhipov A, Freddolino PL, Schulten K. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure (London, England : 1993). 14: 1767-77. PMID 17161367 DOI: 10.1016/J.Str.2006.10.003  1
2006 Arkhipov A, Freddolino PL, Imada K, Namba K, Schulten K. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal. 91: 4589-97. PMID 16997871 DOI: 10.1529/Biophysj.106.093443  1
2006 Freddolino PL, Dittrich M, Schulten K. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal. 91: 3630-9. PMID 16935961 DOI: 10.1529/Biophysj.106.088609  1
2006 Lu D, Aksimentiev A, Shih AY, Cruz-Chu E, Freddolino PL, Arkhipov A, Schulten K. The role of molecular modeling in bionanotechnology. Physical Biology. 3: S40-53. PMID 16582464 DOI: 10.1088/1478-3975/3/1/S05  1
2006 Spijker P, Vaidehi N, Freddolino PL, Hilbers PA, Goddard WA. Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist. Proceedings of the National Academy of Sciences of the United States of America. 103: 4882-7. PMID 16551744 DOI: 10.1073/Pnas.0511329103  1
2006 Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure (London, England : 1993). 14: 437-49. PMID 16531228 DOI: 10.1016/J.Str.2005.11.014  1
2006 Shih AY, Arkhipov A, Freddolino PL, Schulten K. Coarse grained protein-lipid model with application to lipoprotein particles. The Journal of Physical Chemistry. B. 110: 3674-84. PMID 16494423 DOI: 10.1021/Jp0550816  1
2005 Dittrich M, Freddolino PL, Schulten K. When light falls in LOV: a quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. The Journal of Physical Chemistry. B. 109: 13006-13. PMID 16852614 DOI: 10.1021/Jp050943O  1
2004 Kalani MY, Vaidehi N, Hall SE, Trabanino RJ, Freddolino PL, Kalani MA, Floriano WB, Kam VW, Goddard WA. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proceedings of the National Academy of Sciences of the United States of America. 101: 3815-20. PMID 14999101 DOI: 10.1073/Pnas.0400100101  1
2004 Freddolino PL, Kalani MY, Vaidehi N, Floriano WB, Hall SE, Trabanino RJ, Kam VW, Goddard WA. Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists. Proceedings of the National Academy of Sciences of the United States of America. 101: 2736-41. PMID 14981238 DOI: 10.1073/Pnas.0308751101  1
2002 Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA. Prediction of structure and function of G protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America. 99: 12622-7. PMID 12351677 DOI: 10.1073/Pnas.122357199  1
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