Anton is a special purpose supercomputer for biomolecular simulation designed and constructed by D. E. Shaw Research (DESRES). PSC's current system is known as Anton 2 and is a successor to the original Anton 1 machine hosted here.
Anton 2, the next-generation Anton supercomputer, is a 128 node system, made available without cost by DESRES for non-commercial research use by US universities and other not-for-profit institutions, and is hosted by PSC with support from the NIH National Institute of General Medical Sciences. It replaced the original Anton 1 system in the fall of 2016.
Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than was previously accessible to computational study. The MD research community is using the Anton 2 machine at PSC to investigate important biological phenomena that due to their intrinsically long time scales have been outside the reach of even the most powerful general-purpose scientific computers. Application areas include biomolecular energy transformation, ion channel selectivity and gating, drug interactions with proteins and nucleic acids, protein folding and protein-membrane signaling.
Anton 2 is allocated annually via a Request for Proposal with proposals reviewed by a committee convened by the National Research Council at the National Academies. To qualify for an allocation on Anton 2, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution.
Applications are now being accepted for allocations to begin in December 2019. The application deadline is Thursday, June 13, 2019.
Anton End User Agreement
All users who are awarded time on Anton2 must complete the Anton End User Agreement (EUA) acknowledging that they have read and understood their responsibilities as an Anton2 user and agree to comply. Once it is signed, return the EUA to firstname.lastname@example.org.
Acknowledgement in publications
Please use the following paragraph (or similiar) to cite your work conducted on Anton. Proper acknowledgment is critical for our ability to solicit continued funding for the project.
Acknowledgement for Anton 2
Anton 2 computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton 2 machine at PSC was generously made available by D.E. Shaw Research.
The proper citation for Anton 2 is:
Shaw, David E., J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, et al. “Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer,” 41–53. IEEE, 2014. doi:10.1109/SC.2014.9.
Acknowledgement for Anton 1
Anton computer time was provided by the Pittsburgh Supercomputing Center (PSC) through Grant R01GM116961 from the National Institutes of Health. The Anton machine at PSC was generously made available by D.E. Shaw Research.
The proper citation for the Anton machine is
Millisecond-Scale Molecular Dynamics Simulations on Anton, D. E. Shaw et al., Proceedings of the ACM/IEEE Conference on Supercomputing (SC09), Portland, Oregon (2009).
See project summaries, including trajectory files, for some Anton 1 research.
Here are highlights of just some of the groundbreaking research enabled by Anton:
Molecular mechanisms of arrestin activation - Simulations provide a structural foundation for the design of functionally selective ligands that lead to particular GPCR signaling profiles. N. Latorraca and R. Dror. doi:10.1038/s41586-018-0077-3
Uncovering new ways to target flu viruses - A conserved amino acid could provide a target toward a universal vaccine for viruses. Xingcheng Lin, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and Jose Onuchic. doi:10.1073/pnas.1805442115.
Kink formation is required for lateral gating in BamA - Simulations of BamA reveal a dynamic gating between the N- and C-terminal strands at the barrel seam. Using free-energy calculations and mutagenesis experiments, it was determined that the C-terminus has to kink inward for efficient opening. lateral gating in BamA. Karl Lundquist, Jeremy Bakelar, Nicholas Noinaj, and JC Gumbart. doi:10.1073/pnas.1722530115
World’s Tiniest Test Tubes in Alzheimer’s Protein Simulation - Simulations of plaque-forming beta amyloid molecules offer insights towards possible Alzheimer’s drug therapies. From PSC's Science Highlights Fall 2018. G. Eskici and P.H. Axelsen. doi:10.1021/acs.langmuir.7b04192.
"Sticky and Loose Ends” Shed Light on Heart Health - Simulations show APOA1 protein ends link to hold together “the good cholesterol”. From PSC's Science Highlights Fall 2018. Mohsen Pourmousa, Richard Pastor, Jere Segrest, et. al. doi: 10.1073/pnas.1721181115
Locked, Not Loaded - New target in HIV-1 replication. Simulations may lead to more effective anti-maturation drugs to fight AIDS and possibly other viral diseases. From PSC's Science Highlights Spring 2018. J. Perilla et al. doi:10.1038/s41467-017-01856-y.
Inner Space - Work on Anton highlights the importance of empty space for protein function. Simulations of T4 lysozyme L99A show that big gaps opened up in the protein, which “let in” molecules roughly the size of drug molecules. From PSC's Science Highlights Fall 2017.
Hooked Up - Simulations on Anton discover the critical role disulfides play in holding together MCoTI-II, a natural pesticide that would fall apart without disulfide bridges. From PSC's Science Highlights Spring 2017.
This article was highlighted in the cover of Nature Physics and discussed in the following article: Metzler R, News and Views Protein physics: Forever ageing, Nature Phys., 2016, 12, 113–114, doi:10.1038/nphys3585.
Zhang, Yi, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson, and Norelle L. Daly. "Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide". Biophysical Journal 110, no. 8 (April 2016): 1744–52. doi:10.1016/j.bpj.2016.03.027.
This article was featured on the cover of the Biophysical Journal.
Sodt, Alexander J., Richard W. Pastor, and Edward Lyman. “Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin.” Biophysical Journal 109, no. 5 (September 2015): 948–55. doi:10.1016/j.bpj.2015.07.036
This study was featured on the cover of the Biophysical Journal and highlighted as New and Notable: http://www.cell.com/biophysj/abstract/S0006-3495(15)00772-9
A TUG Felt Elsewhere - Anton simulations show how drug-producing enzyme is enhanced by changes far from reactive site, from PSC’s Projects in Scientific Computing, Fall 2014.
Two Steps Forward, One Step Back - molecular dynamics simulations disclose how water leaving and then re-entering the potassium channel delays its return to the active state, from PSC's Projects in Scientific Computing, Spring 2014.
A Movie is Worth a Million Pictures - structural dynamics simulations illuminate the mechanisms of sodium-coupled substrate binding/release in an aspartate transporter, from PSC's 2013 annual report, Projects in Scientific Computing
Epic Microseconds - four projects yielding invaluable insights into the structure and function of proteins from PSC's 2012 annual report, Projects in Scientific Computing
Protein Research Leaps Forward - four projects in MD simulation from PSC's 2011 annual report, Projects in Scientific Computing
Atomic-Level Characterization of the Structural Dynamics of Proteins - This paper, published in Science, details the first millisecond MD simulation on Anton.
Shaw, David E., Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, Willy Wriggers. "Atomic-Level Characterization of the Structural Dynamics of Proteins" Science 15 Oct 2010: 341-346 DOI: 10.1126/science.1187409
Millisecond-scale molecular dynamics simulations on Anton - This paper (Gordon Bell prize winner for best paper at SC09 ) contains measurements of energy conservation on Anton that you can use to compare with your own simulations.
Publications for research that made use of Anton or Anton 2 at PSC:
Balusek, Curtis, Hyea Hwang, Chun Hon Lau, Karl Lundquist, Anthony Hazel, Anna Pavlova, Diane L. Lynch, Patricia H. Reggio, Yi Wang, and James C. Gumbart. “Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.” Journal of Chemical Theory and Computation, June 20, 2019. https://doi.org/10.1021/acs.jctc.9b00160.
Cao, Shufen, Stacey Chung, SoonJeung Kim, Zhenlu Li, Danny Manor, and Matthias Buck. “K-Ras G-Domain Binding with Signaling Lipid Phosphatidyl Inositol (4,5) Phosphate (PIP2): Membrane Association, Protein Orientation and Function.” Journal of Biological Chemistry 294 (February 21, 2019): 7064–84. https://doi.org/10.1074/jbc.RA118.004021.
Duff, Henry J, Sergei Y Noskov, Danielle Muruve, German Perlovic, Marina Ol Khovich, Angelica Sharapova, Brenda Gerull, Jiqing Guo, Meryuvert Kudaibergenova, and Laura Perissinotti. “The Pore-Lipid Interface: Role of Amino Acid Determinants of Lipophilic Access by Ivabradine to the HERG1 Pore Domain.” Molecular Pharmacology, June 10, 2019, mol.118.115642. https://doi.org/10.1124/mol.118.115642.
Ellis-Guardiola, Ken, Huan Rui, Ryan L Beckner, Poonam Srivastava, Narayanasami Sukumar, Benoît Roux, and Jared C. Lewis. “Crystal Structure and Conformational Dynamics of Pyrococcus Furiosus Prolyl Oligopeptidase.” Biochemistry 58, no. 12 (February 20, 2019): 1616–1626. https://doi.org/10.1021/acs.biochem.9b00031.
Freites, J. Alfredo, Karin L. Németh-Cahalan, James E. Hall, and Douglas J. Tobias. “Cooperativity and Allostery in Aquaporin 0 Regulation by Ca2+.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1861, no. 5 (May 2019): 988–96. https://doi.org/10.1016/j.bbamem.2019.02.007.
Immadisetty, Kalyan, Jeevapani Hettige, and Mahmoud Moradi. “Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter.” ACS Central Science 5, no. 1 (n.d.): 43–56. https://doi.org/DOI: 10.1021/acscentsci.8b00480.
Jekhmane, Shehrazade, João Medeiros-Silva, Jing Li, Felix Kümmerer, Christoph Müller-Hermes, Marc Baldus, Benoît Roux, and Markus Weingarth. “Shifts in the Selectivity Filter Dynamics Cause Modal Gating in K+ Channels.” Nature Communications 10, no. 123 (December 2019). https://doi.org/10.1038/s41467-018-07973-6.
Lacroix, Jerome. “A Mechanism for the Activation of the Mechanosensitive Piezo1 Channel by the Small Molecule Yoda1.” Nature Communications, n.d.
Liao, Chenyi, Victor May, and Jianing Li. “Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics.” In G Protein-Coupled Receptor Signaling, edited by Mario Tiberi, 1947:3–19. New York, NY: Springer New York, 2019. https://doi.org/10.1007/978-1-4939-9121-1_1.
Majumdar, Bibhab Bandhu, Vera Prytkova, Eric K. Wong, J. Alfredo Freites, Douglas J. Tobias, and Matthias Heyden. “Role of Conformational Flexibility in Monte Carlo Simulations of Many-Protein Systems.” Journal of Chemical Theory and Computation 15, no. 2 (February 12, 2019): 1399–1408. https://doi.org/10.1021/acs.jctc.8b00894.
Martynowycz, Michael W., Amy Rice, Konstantin Andreev, Thatyane M. Nobre, Ivan Kuzmenko, Jeff Wereszczynski, and David Gidalevitz. “Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37.” ACS Infectious Diseases, May 24, 2019. https://doi.org/10.1021/acsinfecdis.9b00066.
McGraw, Claire, Lewen Yang, Ilya Levental, Edward Lyman, and Anne Skaja Robinson. “Membrane Cholesterol Depletion Reduces Downstream Signaling Activity of the Adenosine A2A Receptor.” Biochimica et Biophysica Acta (BBA) - Biomembranes 1861, no. 4 (April 2019): 760–67. https://doi.org/10.1016/j.bbamem.2019.01.001.
Monje-Galvan, Viviana, Linnea Warburton, and Jeffery B. Klauda. “Setting Up All-Atom Molecular Dynamics Simulations to Study the Interactions of Peripheral Membrane Proteins with Model Lipid Bilayers.” In Intracellular Lipid Transport, edited by Guillaume Drin, 1949:325–39. New York, NY: Springer New York, 2019. https://doi.org/10.1007/978-1-4939-9136-5_22.
Nguyen, Phuong T., Kevin R. DeMarco, Igor Vorobyov, Colleen E. Clancy, and Vladimir Yarov-Yarovoy. “Structural Basis for Antiarrhythmic Drug Interactions with the Human Cardiac Sodium Channel.” Proceedings of the National Academy of Sciences 116, no. 8 (February 19, 2019): 2945–54. https://doi.org/10.1073/pnas.1817446116.
Prigozhin, Maxim B., Yi Zhang, Klaus Schulten, Martin Gruebele, and Taras V. Pogorelov. “Fast Pressure-Jump All-Atom Simulations and Experiments Reveal Site-Specific Protein Dehydration-Folding Dynamics.” Proceedings of the National Academy of Sciences 116, no. 12 (March 19, 2019): 5356–61. https://doi.org/10.1073/pnas.1814927116.
Rajagopal, Nandhini, Flaviyan Jerome Irudayanathan, and Shikha Nangia. “Palmitoylation of Claudin-5 Proteins Influences Their Lipid Domain Affinity and Tight Junction Assembly at the Blood–Brain Barrier Interface.” The Journal of Physical Chemistry B 123, no. 5 (January 28, 2019): 983–93. https://doi.org/10.1021/acs.jpcb.8b09535.
Rice, Amy. “Toward a Comprehensive Atomistic View of Bacterial Outer Membrane Remodeling and Antimicrobial Peptide Susceptibility.” Ph.D., Physics, Illinois Institute of Technology, 2019.
Smaga, Sarah Sierra, Chaoyi Xu, Brady James Summers, Katherine Marie Digianantonio, Juan Roberto Perilla, and Yong Xiong. “MxB Restricts HIV-1 by Targeting the Tri-Hexamer Interface of the Viral Capsid.” Structure, 2019, in press. https://doi.org/10.1101/444067.
Taylor, Bryn C., Christopher T. Lee, and Rommie E. Amaro. “Structural Basis for Ligand Modulation of the CCR2 Conformational Landscape.” Proceedings of the National Academy of Sciences116, no. 17 (April 23, 2019): 8131–36. https://doi.org/10.1073/pnas.1814131116.
Walker, Alice R., Baddam, Nikhil, and Cisneros, G. Andres. “Unfolding Pathways of Hen Egg White Lysozyme in Ethanol.” J. Physical Chemistry B 123, no. 15 (2019): 3267–71. https://doi.org/DOI: 10.1021/acs.jpcb.9b01694.
Weiner, Michael D., and Gerald W. Feigenson. “Molecular Dynamics Simulations Reveal Leaflet Coupling in Compositionally Asymmetric Phase-Separated Lipid Membranes.” The Journal of Physical Chemistry B 123, no. 18 (May 9, 2019): 3968–75. https://doi.org/10.1021/acs.jpcb.9b03488.
Wildermuth, Kyle D., Viviana Monje-Galvan, Linnea M. Warburton, and Jeffery B. Klauda. “Effect of Membrane Lipid Packing on Stable Binding of the ALPS Peptide.” Journal of Chemical Theory and Computation 15, no. 2 (February 12, 2019): 1418–29. https://doi.org/10.1021/acs.jctc.8b00945.
Winogradoff, David, and Aleksei Aksimentiev. “Molecular Mechanism of Spontaneous Nucleosome Unraveling.” Journal of Molecular Biology 431, no. 2 (January 2019): 323–35. https://doi.org/10.1016/j.jmb.2018.11.013.
Wong, Eric K., Vera Prytkova, J. Alfredo Freites, Carter T. Butts, and Douglas J. Tobias. “Molecular Mechanism of Aggregation of the Cataract-Related ΓD-Crystallin W42R Variant from Multiscale Atomistic Simulations.” Biochemistry, August 8, 2019. https://doi.org/10.1021/acs.biochem.9b00208.
- Chakraborty, Kaushik, Myungshim Kang, and Sharon M. Loverde. “Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning.” The Journal of Physical Chemistry B 122, no. 50 (December 20, 2018): 11827–40. https://doi.org/10.1021/acs.jpcb.8b07881.
- Cheng, Mary Hongying, Cihan Kaya, and Ivet Bahar. “Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter.” The Journal of Physical Chemistry B, December 26, 2017. doi: 10.1021/acs.jpcb.7b10340.
- Debiec, Karl T., Matthew J. Whitley, Leonardus M.I. Koharudin, Lillian T. Chong, and Angela M. Gronenborn. “Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.” Biophysical Journal 114, no. 4 (February 2018): 839–55. doi: 10.1016/j.bpj.2018.01.001.
- DeMarco, Kevin R., Slava Bekker, Colleen E. Clancy, Sergei Y. Noskov, and Igor Vorobyov. “Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker D-Sotalol with All-Atom Simulations.” Frontiers in Pharmacology 9 (February 1, 2018). doi: 10.3389/fphar.2018.00026.
- Dick, Robert A., Kaneil K. Zadrozny, Chaoyi Xu, Florian K. M. Schur, Terri D. Lyddon, Clifton L. Ricana, Jonathan M. Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, August 1, 2018. doi: 10.1038/s41586-018-0396-4
- Eskici, Gozde, and Paul H. Axelsen. “Mass Exchange and Equilibration Processes in AOT Reverse Micelles.” Langmuir 34, no. 7 (February 20, 2018): 2522–30. doi: 10.1021/acs.langmuir.7b04192.
- Flood, Emelie, Céline Boiteux, and Toby W. Allen. “Selective Ion Permeation Involves Complexation with Carboxylates and Lysine in a Model Human Sodium Channel.” Edited by Alexander MacKerell. PLOS Computational Biology 14, no. 9 (September 12, 2018): e1006398. doi: 10.1371/journal.pcbi.1006398
- Gołaś, Ewa I., Magdalena Mozolewska, Pawel Krupa, Cezary Czaplewski, Adam Scheraga, and Adam Liwo. “Use of Coarse-Grained and All-Atom Molecular Dynamics to Study Hsp70 and Hsp40 Chaperone Action.” In Frontiers in Structural Biology, 1:23–46, 2018.
- Gumbart, James C., Martin B. Ulmschneider, Anthony Hazel, Stephen H. White, and Jakob P. Ulmschneider. “Computed Free Energies of Peptide Insertion into Bilayers Are Independent of Computational Method.” The Journal of Membrane Biology, March 8, 2018. doi: 10.1007/s00232-018-0026-y.
- Heppner, David E., Christopher M. Dustin, Chenyi Liao, Milena Hristova, Carmen Veith, Andrew C. Little, Bethany A. Ahlers, et al. “Direct Cysteine Sulfenylation Drives Activation of the Src Kinase.” Nature Communications 9, no. 1 (December 2018). https://doi.org/10.1038/s41467-018-06790-1.
- Hoogerheide, David P., Sergei Yu. Noskov, Adam J. Kuszak, Susan K. Buchanan, Tatiana K. Rostovtseva, and Hirsh Nanda. “Structure of Voltage-Dependent Anion Channel-Tethered Bilayer Lipid Membranes Determined Using Neutron Reflectivity.” Acta Crystallographica Section D Structural Biology 74, no. 12 (December 1, 2018): 1219–32. https://doi.org/10.1107/S2059798318011749
- Islam, Rafique M., Mohsen Pourmousa, Denis Sviridov, Scott M. Gordon, Edward B. Neufeld, Lita A. Freeman, B. Scott Perrin, Richard W. Pastor, and Alan T. Remaley. “Structural Properties of Apolipoprotein A-I Mimetic Peptides That Promote ABCA1-Dependent Cholesterol Efflux.” Scientific Reports 8, no. 1 (December 2018). doi: 10.1038/s41598-018-20965-2.
- Iyer, Sahithya S., Madhusmita Tripathy, and Anand Srivastava. “Fluid Phase Coexistence in Biological Membrane: Insights from Local Nonaffine Deformation of Lipids.” Biophysical Journal 115, no. 1 (July 2018): 117–28. doi: 10.1016/j.bpj.2018.05.021
- Kimanius, D., E. Lindahl, and M. Andersson. “Uptake Dynamics in the Lactose Permease (LacY) Membrane Protein Transporter.” Scientific Reports 8, no. 1 (December 2018). https://doi.org/10.1038/s41598-018-32624-7.
- Latorraca, Naomi R., Jason K. Wang, Brian Bauer, Raphael J. L. Townshend, Scott A. Hollingsworth, Julia E. Olivieri, H. Eric Xu, Martha E. Sommer, and Ron O. Dror. “Molecular Mechanism of GPCR-Mediated Arrestin Activation.” Nature 557, no. 7705 (May 2018): 452–56. doi: 10.1038/s41586-018-0077-3.
- Lee, Byoung-Cheol, George Khelashvili, Maria Falzone, Anant K. Menon, Harel Weinstein, and Alessio Accardi. “Gating Mechanism of the Extracellular Entry to the Lipid Pathway in a TMEM16 Scramblase.” Nature Communications 9, no. 1 (December 2018). doi: 10.1038/s41467-018-05724-1.
- Lee, Hui Sun, Yeonock Oh, Mahn-Joo Kim, and Wonpil Im. “Molecular Basis of Aqueous-like Activity of Lipase Treated with Glucose-Headed Surfactant in Organic Solvent.” The Journal of Physical Chemistry B 122, no. 47 (November 29, 2018): 10659–68. https://doi.org/10.1021/acs.jpcb.8b07686.
- Li, Zhen-Lu, Priyanka Prakash, and Matthias Buck. “A ‘Tug of War’ Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane.” ACS Central Science 4, no. 2 (February 28, 2018): 298–305. doi: 10.1021/acscentsci.7b00593.
- Lin, Xingcheng, Jeffrey K. Noel, Qinghua Wang, Jianpeng Ma, and José N. Onuchic. “Atomistic Simulations Indicate the Functional Loop-to-Coiled-Coil Transition in Influenza Hemagglutinin Is Not Downhill.” Proceedings of the National Academy of Sciences 115, no. 34 (August 21, 2018): E7905–13. doi: 10.1073/pnas.1805442115.
- Liu, Fangming, Hannah Hoag, Chun Wu, Haizhou Liu, Hua Yin, Jianjun Dong, Zhonghua Qian, Feng Miao, Ming Liu, and Jinlai Miao. “Experimental and Simulation Identification of Xanthohumol as an Inhibitor and Substrate of ABCB1.” Applied Sciences 8, no. 5 (April 27, 2018): 681. doi: 10.3390/app8050681.
- Lundquist, Karl, Jeremy Bakelar, Nicholas Noinaj, and James C. Gumbart. “C-Terminal Kink Formation Is Required for Lateral Gating in BamA.” Proceedings of the National Academy of Sciences, August 7, 2018, 201722530. doi: 10.1073/pnas.1722530115.
- Marino, Kristen A., and Marta Filizola. “Investigating Small-Molecule Ligand Binding to G Protein- Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations.” In Computational Methods for GPCR Drug Discovery, edited by Alexander Heifetz, 1705:351–64. New York, NY: Springer New York, 2018. doi: 10.1007/978-1-4939-7465-8_17.
- Min, Duyoung, Robert E. Jefferson, Yifei Qi, Jing Yang Wang, Mark A. Arbing, Wonpil Im, and James U. Bowie. “Unfolding of a ClC Chloride Transporter Retains Memory of Its Evolutionary History.” Nature Chemical Biology 14, no. 5 (May 2018): 489–96. doi: 10.1038/s41589-018-0025-4.
- Monje-Galvan, Viviana, and Jeffery B. Klauda. “Preferred Binding Mechanism of Osh4’s ALPS Motif, Insights From Molecular Dynamics.” The Journal of Physical Chemistry B, October 3, 2018. doi: 10.1021/
- Montgomery, David, Alexandra Campbell, Holli-Joi Sullivan, and Chun Wu. “Molecular Dynamics Simulation of Biased Agonists at the Dopamine D2 Receptor Suggests the Mechanism of Receptor Functional Selectivity.” Journal of Biomolecular Structure and Dynamics, August 19, 2018, 1–49. doi: 10.1080/07391102.2018.1513378.
- Newmister, Sean A., Shasha Li, Marc Garcia-Borràs, Jacob N. Sanders, Song Yang, Andrew N. Lowell, Fengan Yu, et al. “Structural Basis of the Cope Rearrangement and Cyclization in Hapalindole Biogenesis.” Nature Chemical Biology, March 12, 2018. doi: 10.1038/s41589-018-0003-x.
- Ohmann, Alexander, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser, and Aleksei Aksimentiev. “A Synthetic Enzyme Built from DNA Flips 107 Lipids per Second in Biological Membranes.” Nature Communications 9, no. 1 (December 2018). https://doi.org/10.1038/s41467-018-04821-5.
- Palermo, Giulia, Janice S. Chen, Clarisse G. Ricci, Ivan Rivalta, Martin Jinek, Victor S. Batista, Jennifer A. Doudna, and J. Andrew McCammon. “Key Role of the REC Lobe during CRISPR–Cas9 Activation by ‘Sensing’, ‘Regulating’, and ‘Locking’ the Catalytic HNH Domain.” Quarterly Reviews of Biophysics 51 (2018). https://doi.org/10.1017/S0033583518000070.
- Pino-Angeles, Almudena, and Themis Lazaridis. “Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores.” Biophysical Journal 114, no. 12 (June 2018): 2865–74. doi: 10.1016/j.bpj.2018.05.006
- Pourmousa, Mohsen, and Richard W. Pastor. “Molecular Dynamics Simulations of Lipid Nanodiscs.” Biochimica et Biophysica Acta (BBA) - Biomembranes, May 2018. doi: 10.1016/j.bbamem.2018.04.015.
- Pourmousa, Mohsen, Hyun D. Song, Yi He, Jay W. Heinecke, Jere P. Segrest, and Richard W. Pastor. “Tertiary Structure of Apolipoprotein A-I in Nascent High-Density Lipoproteins.” Proceedings of the National Academy of Sciences 115, no. 20 (May 15, 2018): 5163–68. doi: 10.1073/pnas.1721181115.
- Prakash, Priyanka, Douglas Litwin, Hong Liang, Suparna Sarkar-Banerjee, Drew Dolino, Yong Zhou, John F. Hancock, Vasanthi Jayaraman, and Alemayehu A. Gorfe. “Dynamics of Membrane-Bound G12V KRAS Investigated by Simulation and Single Molecule FRET in Native Nanodiscs.” Biophysical Journal, December 2018. https://doi.org/10.1016/j.bpj.2018.12.011.
- Rice, Amy, and Jeff Wereszczynski. “Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses.” Biophysical Journal 114, no. 6 (March 2018): 1389–99. doi: 10.1016/j.bpj.2018.02.006
- Sader, Safaa, Kumar Anant, and Chun Wu. “To Probe Interaction of Morphine and IBNtxA with 7TM and 6TM Variants of the Human μ-Opioid Receptor Using All-Atom Molecular Dynamics Simulations with an Explicit Membrane.” Physical Chemistry Chemical Physics 20, no. 3 (2018): 1724–41. doi: 10.1039/C7CP06745C.
- Shahul Hameed, Umar F, Chenyi Liao, Anand K Radhakrishnan, Franceline Huser, Safia S Aljedani, Xiaochuan Zhao, Afaque A Momin, et al. “H-NS Uses an Autoinhibitory Conformational Switch for Environment-Controlled Gene Silencing.” Nucleic Acids Research, December 28, 2018. https://doi.org/10.1093/nar/gky1299.
- Sparks, Samuel, Deniz B. Temel, Michael P. Rout, and David Cowburn. “Deciphering the ‘Fuzzy’ Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering.” Structure 26, no. 3 (March 2018): 477–484.e4. doi: 10.1016/j.str.2018.01.010.
- Tran, Kelly. “Reduction Potential Properties of Electron Transfer Proteins.” Georgetown University, Ph.D. Thesis, 2018.
- Weiner, Michael D. “Coupling and Clustering in Molecular Dynamics Simulations of Lipid Membrane Biophysics.” Cornell Univ., 2018.
- Wong, Eric K. “Modeling the Structure and Dynamics of Gamma-Crystallins and Their Cataract-Related Variants,” 2018. Ph.D. Thesis, Univ. of California, Irvine.
- Yu, Alvin, and Albert Y. Lau. “Glutamate and Glycine Binding to the NMDA Receptor.” Structure, June 2018. doi: 10.1016/j.str.2018.05.004.
- Yu, Alvin, Héctor Salazar, Andrew J.R. Plested, and Albert Y. Lau. “Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics.” Neuron 97, no. 1 (January 2018): 139–149.e4. doi: 10.1016/j.neuron.2017.11.024.
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