| Year |
Citation |
Score |
| 2024 |
Dinh T, Tber Z, Rey JS, Mengshetti S, Annamalai AS, Haney R, Briganti L, Amblard F, Fuchs JR, Cherepanov P, Kim K, Schinazi RF, Perilla JR, Kim B, Kvaratskhelia M. The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. Biorxiv : the Preprint Server For Biology. PMID 38328097 DOI: 10.1101/2024.01.26.577387 |
0.318 |
|
| 2023 |
Deshpande A, Bryer AJ, Andino J, Shi J, Hong J, Torres C, Harel S, Francis AC, Perilla JR, Aiken C, Rousso I. Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection. Biorxiv : the Preprint Server For Biology. PMID 37808653 DOI: 10.1101/2023.09.29.560083 |
0.394 |
|
| 2023 |
Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Nature Communications. 14: 5614. PMID 37699872 DOI: 10.1038/s41467-023-41197-7 |
0.752 |
|
| 2023 |
Krebs AS, Liu HF, Zhou Y, Rey JS, Levintov L, Shen J, Howe A, Perilla JR, Bartesaghi A, Zhang P. Molecular architecture and conservation of an immature human endogenous retrovirus. Nature Communications. 14: 5149. PMID 37620323 DOI: 10.1038/s41467-023-40786-w |
0.31 |
|
| 2023 |
Krebs AS, Liu HF, Zhou Y, Rey JS, Levintov L, Shen J, Howe A, Perilla JR, Bartesaghi A, Zhang P. Molecular architecture and conservation of an immature human endogenous retrovirus. Biorxiv : the Preprint Server For Biology. PMID 37333227 DOI: 10.1101/2023.06.07.544027 |
0.346 |
|
| 2023 |
Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, ... ... Perilla JR, et al. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proceedings of the National Academy of Sciences of the United States of America. 120: e2202815120. PMID 36943880 DOI: 10.1073/pnas.2202815120 |
0.768 |
|
| 2023 |
Sarkar S, Zadrozny KK, Zadorozhnyi R, Russell RW, Quinn CM, Kleinpeter A, Ablan S, Meshkin H, Perilla JR, Freed EO, Ganser-Pornillos BK, Pornillos O, Gronenborn AM, Polenova T. Structural basis of HIV-1 maturation inhibitor binding and activity. Nature Communications. 14: 1237. PMID 36871077 DOI: 10.1038/s41467-023-36569-y |
0.546 |
|
| 2023 |
Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. Mbio. e0356022. PMID 36744954 DOI: 10.1128/mbio.03560-22 |
0.383 |
|
| 2022 |
Balasubramaniam M, Davids BO, Bryer A, Xu C, Thapa S, Shi J, Aiken C, Pandhare J, Perilla JR, Dash C. HIV-1 mutants that escape the cytotoxic T-lymphocytes are defective in viral DNA integration. Pnas Nexus. 1: pgac064. PMID 35719891 DOI: 10.1093/pnasnexus/pgac064 |
0.746 |
|
| 2022 |
Kraus J, Russell RW, Kudryashova E, Xu C, Katyal N, Perilla JR, Kudryashov DS, Polenova T. Magic angle spinning NMR structure of human cofilin-2 assembled on actin filaments reveals isoform-specific conformation and binding mode. Nature Communications. 13: 2114. PMID 35440100 DOI: 10.1038/s41467-022-29595-9 |
0.707 |
|
| 2022 |
Bryer AJ, Reddy T, Lyman E, Perilla JR. Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. Plos Computational Biology. 18: e1009781. PMID 35041642 DOI: 10.1371/journal.pcbi.1009781 |
0.402 |
|
| 2021 |
Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P. Structure of native HIV-1 cores and their interactions with IP6 and CypA. Science Advances. 7: eabj5715. PMID 34797722 DOI: 10.1126/sciadv.abj5715 |
0.744 |
|
| 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 |
0.338 |
|
| 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 |
0.603 |
|
| 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 |
0.343 |
|
| 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 |
0.776 |
|
| 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 |
0.721 |
|
| 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 |
0.594 |
|
| 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 |
0.784 |
|
| 2020 |
Gonzalez-Arias FA, Reddy TJ, Perilla JR. Unveiling the Structural Properties of HIV-1 Vesicle from Coarse-Grain Molecular Dynamics Simulations Biophysical Journal. 118: 299a. DOI: 10.1016/j.bpj.2019.11.1696 |
0.402 |
|
| 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 |
0.776 |
|
| 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 |
0.768 |
|
| 2019 |
Reddy T, Perilla JR. Molecular Dynamics Simulations of an Entire HIV Virion Biophysical Journal. 116: 14a. DOI: 10.1016/J.BPJ.2018.11.119 |
0.413 |
|
| 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 |
0.807 |
|
| 2018 |
Hadden JA, Perilla JR. All-atom virus simulations. Current Opinion in Virology. PMID 30181049 DOI: 10.1016/J.Coviro.2018.08.007 |
0.774 |
|
| 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 |
0.73 |
|
| 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 |
0.775 |
|
| 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 |
0.794 |
|
| 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 |
0.363 |
|
| 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 |
0.746 |
|
| 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 |
0.772 |
|
| 2018 |
Xu C, Perilla J. Energetics of Nucleotide Translocation through HIV-1 CA Hexamer Biophysical Journal. 114: 93a. DOI: 10.1016/J.BPJ.2017.11.550 |
0.33 |
|
| 2018 |
Perilla JR. Atomic-Level Characterization of the HIV-1 Capsid and Host-Pathogen Interactions from Molecular Dynamics Simulations Biophysical Journal. 114: 339a. DOI: 10.1016/J.BPJ.2017.11.1895 |
0.408 |
|
| 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 |
0.712 |
|
| 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 |
0.566 |
|
| 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 |
0.598 |
|
| 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 |
0.531 |
|
| 2017 |
Alvarez FJD, He S, Perilla JR, Jang S, Prevelige PE, Engelman A, Schulten K, Scheres S, Zhang P. Cryoem Structure of the Full Length Dynamin-Like MxB at 4.6 Å Resolution Biophysical Journal. 112: 334a. DOI: 10.1016/J.Bpj.2016.11.1808 |
0.397 |
|
| 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 |
0.657 |
|
| 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 |
0.794 |
|
| 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 |
0.491 |
|
| 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 |
0.526 |
|
| 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 |
0.689 |
|
| 2016 |
Goh BC, Perilla JR, Heyrana KJ, England MR, Craven RC, Schulten K. Elucidating the Structure, Dynamics and Functions of an Immature Retrovirus in Atomistic Detail Biophysical Journal. 110: 383a. DOI: 10.1016/J.Bpj.2015.11.2071 |
0.593 |
|
| 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 |
0.484 |
|
| 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 |
0.668 |
|
| 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 |
0.561 |
|
| 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 |
0.502 |
|
| 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 |
0.559 |
|
| 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 |
0.365 |
|
| 2015 |
Himes BA, Cassidy CK, Ma J, Alvarez FJD, Perilla JR, Zhao G, Schulten K, Zhang P. Cryo-Electron Tomography and Computer Simulations Reveal Distinct CheA Kinase Conformation in Bacterial Chemotaxis Signaling Receptor Complex Biophysical Journal. 108: 418a. DOI: 10.1016/J.Bpj.2014.11.2290 |
0.447 |
|
| 2015 |
Cassidy CK, Himes B, Alvarez FJD, Perilla JR, Ma J, Zhao G, Zhang P, Schulten K. Molecular Insights into the Signaling Mechanism of the Histidine Kinase CheA within an Intact Bacterial Chemosensory Array Biophysical Journal. 108: 317a. DOI: 10.1016/J.Bpj.2014.11.1724 |
0.486 |
|
| 2015 |
Perilla JR, Schulten K. Atomistic Characterization of the HIV Capsid from Molecular Dynamics Simulations Biophysical Journal. 108: 209a. DOI: 10.1016/J.Bpj.2014.11.1156 |
0.597 |
|
| 2015 |
Zhang P, Liu C, Perilla JR, Byeon I, Ning J, Ahn J, Aiken C, Gronenborn AM, Polenova T, Schulten K. Cyclophilin a Stabilizes the Mature HIV-1 Capsid through a Novel Non-Canonical Binding Site Biophysical Journal. 108: 190a. DOI: 10.1016/J.Bpj.2014.11.1051 |
0.694 |
|
| 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 |
0.686 |
|
| 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 |
0.5 |
|
| 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 |
0.567 |
|
| 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 |
0.543 |
|
| 2011 |
Perilla JR, Woolf TB. Towards Finding a Better Reaction Coordinate: NtrC and DIMS Biophysical Journal. 100: 534a. DOI: 10.1016/j.bpj.2010.12.3119 |
0.427 |
|
| 2011 |
Perilla JR, Leahy D, Woolf TB. Dynamic Importance Sampling Calculations on ECD Epitelial Growth Factor Receptor Conformational Changes Biophysical Journal. 100: 256a. DOI: 10.1016/J.Bpj.2010.12.1613 |
0.518 |
|
| 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 |
0.566 |
|
| 2009 |
Nagarajan A, Perilla JR, Woolf TB. Understanding the conformational changes in Ca-APTase using Coarse-grained and All-atom simulations with Dynamic Importance Sampling Biophysical Journal. 96: 430a. DOI: 10.1016/J.Bpj.2008.12.2203 |
0.569 |
|
| 2009 |
Perilla JR, Nagarajan A, Beckstein O, Woolf TB. Computing Transitions in Macromolecular Systems: Dynamic Importance Sampling Biophysical Journal. 96: 407a. DOI: 10.1016/J.Bpj.2008.12.2074 |
0.559 |
|
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