Juan R. Perilla, Ph.D. - Publications

Affiliations: 
2017- University of Delaware, Newark, DE, United States 
Area:
General Biophysics, Physical Chemistry, Molecular Biology

44 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 Jones PE, Pérez-Segura C, Bryer AJ, Perilla JR, Hadden-Perilla JA. Molecular dynamics of the viral life cycle: progress and prospects. Current Opinion in Virology. 50: 128-138. PMID 34464843 DOI: 10.1016/j.coviro.2021.08.003  1
2021 Thames T, Bryer AJ, Qiao X, Jeon J, Weed R, Janicki K, Hu B, Gor'kov PL, Hung I, Gan Z, Perilla JR, Chen B. Curvature of the Retroviral Capsid Assembly Is Modulated by a Molecular Switch. The Journal of Physical Chemistry Letters. 7768-7776. PMID 34374542 DOI: 10.1021/acs.jpclett.1c01769  1
2021 Perilla JR, Hadden-Perilla JA, Gronenborn AM, Polenova T. Integrative structural biology of HIV-1 capsid protein assemblies: combining experiment and computation. Current Opinion in Virology. 48: 57-64. PMID 33901736 DOI: 10.1016/j.coviro.2021.03.005  1
2020 Segura CP, Katyal N, González-Arias F, Bryer AJ, Perilla JR, Hadden-Perilla JA. Coronavirus through Delaware's Computational Microscope. Delaware Journal of Public Health. 6: 6-9. PMID 34467099 DOI: 10.32481/djph.2020.07.003  1
2020 González-Arias F, Reddy T, Stone JE, Hadden-Perilla JA, Perilla JR. Scalable Analysis of Authentic Viral Envelopes on FRONTERA. Computing in Science & Engineering. 22: 11-20. PMID 33510584 DOI: 10.1109/mcse.2020.3020508  1
2020 Xu C, Fischer DK, Rankovic S, Li W, Dick RA, Runge B, Zadorozhnyi R, Ahn J, Aiken C, Polenova T, Engelman AN, Ambrose Z, Rousso I, Perilla JR. Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis. Plos Biology. 18: e3001015. PMID 33332391 DOI: 10.1371/journal.pbio.3001015  1
2020 Xu C, Katyal N, Nesterova T, Perilla JR. Molecular determinants of Ebola nucleocapsid stability from molecular dynamics simulations. The Journal of Chemical Physics. 153: 155102. PMID 33092380 DOI: 10.1063/5.0021491  1
2020 Lu M, Russell RW, Bryer AJ, Quinn CM, Hou G, Zhang H, Schwieters CD, Perilla JR, Gronenborn AM, Polenova T. Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR. Nature Structural & Molecular Biology. 27: 863-869. PMID 32901160 DOI: 10.1038/S41594-020-0489-2  1
2020 Wright E, Ferrato M, Bryer AJ, Searles R, Perilla JR, Chandrasekaran S. Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC. Plos Computational Biology. 16: e1007877. PMID 32401799 DOI: 10.1371/journal.pcbi.1007877  1
2020 Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FKM. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. Plos Pathogens. 16: e1008277. PMID 31986188 DOI: 10.1371/journal.ppat.1008277  1
2019 Bryer A, Hadden-Perilla JA, Stone JE, Perilla JR. High-performance analysis of biomolecular containers to measure small-molecule transport, trans bilayer lipid diffusion, and protein cavities. Journal of Chemical Information and Modeling. PMID 31525965 DOI: 10.1021/acs.jcim.9b00324  1
2019 Huang PT, Summers BJ, Xu C, Perilla JR, Malikov V, Naghavi MH, Xiong Y. FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking. Cell Reports. PMID 31422020 DOI: 10.1016/J.Celrep.2019.07.079  1
2019 Cingolani G, McCauley M, Lobley A, Bryer AJ, Wesolowski J, Greco DL, Lokareddy RK, Ronzone E, Perilla JR, Paumet F. Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA. Nature Communications. 10: 2747. PMID 31227715 DOI: 10.2210/Pdb6E6A/Pdb  1
2019 Smaga SS, Xu C, Summers BJ, Digianantonio KM, Perilla JR, Xiong Y. MxB Restricts HIV-1 by Targeting the Tri-hexamer Interface of the Viral Capsid. Structure (London, England : 1993). PMID 31155311 DOI: 10.1016/J.Str.2019.04.015  1
2018 Quinn CM, Wang M, Fritz MP, Runge B, Ahn J, Xu C, Perilla JR, Gronenborn AM, Polenova T. Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 30333189 DOI: 10.1073/Pnas.1800796115  1
2018 Hadden JA, Perilla JR. All-atom virus simulations. Current Opinion in Virology. PMID 30181049 DOI: 10.1016/J.Coviro.2018.08.007  1
2018 Dick RA, Zadrozny KK, Xu C, Schur FKM, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser-Pornillos BK, Johnson MC, Pornillos O, Vogt VM. Author Correction: Inositol phosphates are assembly co-factors for HIV-1. Nature. PMID 30158708 DOI: 10.1038/S41586-018-0505-4  1
2018 Dick RA, Zadrozny KK, Xu C, Schur FKM, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser-Pornillos BK, Johnson MC, Pornillos O, Vogt VM. Inositol phosphates are assembly co-factors for HIV-1. Nature. PMID 30069050 DOI: 10.1038/S41586-018-0396-4  1
2018 Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K. All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. Elife. 7. PMID 29708495 DOI: 10.7554/Elife.32478  1
2018 Martin JL, Mendonça L, Marusinec R, Zuczek J, Angert I, Blower RJ, Mueller JD, Perilla JR, Zhang W, Mansky LM. Critical Role of the HTLV-1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly. Journal of Virology. PMID 29695435 DOI: 10.1128/Jvi.00333-18  0.12
2018 Hadden JA, Perilla JR. Molecular Dynamics Simulations of Protein-Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors. Methods in Molecular Biology (Clifton, N.J.). 1762: 245-270. PMID 29594776 DOI: 10.1007/978-1-4939-7756-7_13  1
2018 Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K. Author response: All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits Elife. DOI: 10.7554/Elife.32478.028  1
2017 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, et al. Quenching protein dynamics interferes with HIV capsid maturation. Nature Communications. 8: 1779. PMID 29176596 DOI: 10.1038/S41467-017-01856-Y  1
2017 Rayaprolu V, Moore A, Wang JC, Goh BC, Perilla J, Zlotnick A, Mukhopadhyay S. Length of encapsidated cargo impacts stability and structure of in vitro assembled Alphavirus core-like particles. Journal of Physics. Condensed Matter : An Institute of Physics Journal. PMID 28975896 DOI: 10.1088/1361-648X/Aa90D0  1
2017 Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P. CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. Science Advances. 3: e1701264. PMID 28929138 DOI: 10.1126/Sciadv.1701264  1
2017 Perilla JR, Schulten K. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nature Communications. 8: 15959. PMID 28722007 DOI: 10.1038/Ncomms15959  1
2017 Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P. CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 28181439 DOI: 10.1021/Acs.Jpcb.6B13105  1
2016 Zhang H, Hou G, Lu M, Ahn J, Byeon IL, Langmead CJ, Perilla JR, Hung I, Gor'kov PL, Gan Z, Brey WW, Case DA, Schulten K, Gronenborn AM, Polenova T. HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD. Journal of the American Chemical Society. PMID 27701859 DOI: 10.1021/Jacs.6B08744  1
2016 Perilla JR, Hadden JA, Goh BC, Mayne CG, Schulten K. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. The Journal of Physical Chemistry Letters. PMID 27128262 DOI: 10.1021/Acs.Jpclett.6B00517  1
2016 Heyrana KJ, Goh BC, Perilla JR, Nguyen TN, England MR, Bewley MC, Schulten K, Craven RC. Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly. Journal of Virology. PMID 27053549 DOI: 10.1128/Jvi.00378-16  1
2016 Perilla JR, Gronenborn AM. Molecular Architecture of the Retroviral Capsid. Trends in Biochemical Sciences. PMID 27039020 DOI: 10.1016/J.Tibs.2016.02.009  1
2016 Liu C, Perilla JR, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ahn J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, et al. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nature Communications. 7: 10714. PMID 26940118 DOI: 10.1038/Ncomms10714  1
2015 Cassidy CK, Himes BA, Alvarez FJ, Ma J, Zhao G, Perilla JR, Schulten K, Zhang P. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. Elife. 4. PMID 26583751 DOI: 10.7554/eLife.08419  1
2015 Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IL, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, et al. Dynamic allostery governs cyclophilin A-HIV capsid interplay. Proceedings of the National Academy of Sciences of the United States of America. PMID 26553990 DOI: 10.1073/Pnas.1516920112  1
2015 Goh BC, Perilla JR, England MR, Heyrana KJ, Craven RC, Schulten K. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. Structure (London, England : 1993). PMID 26118533 DOI: 10.1016/J.Str.2015.05.017  1
2015 Perilla JR, Goh BC, Cassidy CK, Liu B, Bernardi RC, Rudack T, Yu H, Wu Z, Schulten K. Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology. 31: 64-74. PMID 25845770 DOI: 10.1016/J.Sbi.2015.03.007  1
2015 Perilla JR, Woolf TB. Computing ensembles of transitions with molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 1215: 237-52. PMID 25330966 DOI: 10.1007/978-1-4939-1465-4_11  1
2015 Cassidy CK, Himes BA, Alvarez FJ, Ma J, Zhao G, Perilla JR, Schulten K, Zhang P. Author response: CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling Elife. DOI: 10.7554/Elife.08419.044  1
2014 Korzeniewska A, Cervenka MC, Jouny CC, Perilla JR, Harezlak J, Bergey GK, Franaszczuk PJ, Crone NE. Ictal propagation of high frequency activity is recapitulated in interictal recordings: effective connectivity of epileptogenic networks recorded with intracranial EEG. Neuroimage. 101: 96-113. PMID 25003814 DOI: 10.1016/J.Neuroimage.2014.06.078  1
2013 Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 497: 643-6. PMID 23719463 DOI: 10.1038/Nature12162  1
2013 Perilla JR, Leahy DJ, Woolf TB. Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors. Proteins. 81: 1113-26. PMID 23348956 DOI: 10.1002/Prot.24257  1
2012 Perilla JR, Woolf TB. Towards the prediction of order parameters from molecular dynamics simulations in proteins. The Journal of Chemical Physics. 136: 164101. PMID 22559464 DOI: 10.1063/1.3702447  1
2011 Perilla JR, Beckstein O, Denning EJ, Woolf TB. Computing ensembles of transitions from stable states: Dynamic importance sampling. Journal of Computational Chemistry. 32: 196-209. PMID 21132840 DOI: 10.1002/Jcc.21564  1
2009 Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. Journal of Molecular Biology. 394: 160-76. PMID 19751742 DOI: 10.1016/J.Jmb.2009.09.009  1
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