Mitochondrial injury and cognitive function in HIV infection and methamphetamine use von Var, Susanna R, Day, Tyler R.C, Vitomirov, Andrej, Smith, Davey M, Soontornniyomkij, Virawudh, Moore, David J, Achim, Cristian L, Mehta, Sanjay R, Pérez-Santiago, Josué

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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments von Madhavi Sastry, G., Adzhigirey, Matvey, Day, Tyler, Annabhimoju, Ramakrishna, Sherman, Woody

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Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction von Zhu, Kai, Day, Tyler, Warshaviak, Dora, Murrett, Colleen, Friesner, Richard, Pearlman, David

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Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring von Zhu, Kai, Borrelli, Kenneth W, Greenwood, Jeremy R, Day, Tyler, Abel, Robert, Farid, Ramy S, Harder, Edward

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AggScore: Prediction of aggregation‐prone regions in proteins based on the distribution of surface patches von Sankar, Kannan, Krystek, Stanley R., Carl, Stephen M., Day, Tyler, Maier, Johannes K. X.

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A hierarchical approach to all-atom protein loop prediction von Jacobson, Matthew P., Pincus, David L., Rapp, Chaya S., Day, Tyler J.F., Honig, Barry, Shaw, David E., Friesner, Richard A.

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The Hydrated Proton at the Water Liquid/Vapor Interface von Petersen, Matt K, Iyengar, Srinivasan S, Day, Tyler J. F, Voth, Gregory A

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Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection von Pérez-Santiago, Josué, Schrier, Rachel D., de Oliveira, Michelli F., Gianella, Sara, Var, Susanna R., Day, Tyler R. C., Ramirez-Gaona, Miguel, Suben, Jesse D., Murrell, Ben, Massanella, Marta, Cherner, Mariana, Smith, Davey M., Ellis, Ronald J., Letendre, Scott L., Mehta, Sanjay R.

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New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies von Farid, Ramy, Day, Tyler, Friesner, Richard A., Pearlstein, Robert A.

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Cerebrospinal fluid cell-free mitochondrial DNA is associated with HIV replication, iron transport, and mild HIV-associated neurocognitive impairment von Mehta, Sanjay R, Pérez-Santiago, Josué, Hulgan, Todd, Day, Tyler R C, Barnholtz-Sloan, Jill, Gittleman, Haley, Letendre, Scott, Ellis, Ronald, Heaton, Robert, Patton, Stephanie, Suben, Jesse D, Franklin, Donald, Rosario, Debralee, Clifford, David B, Collier, Ann C, Marra, Christina M, Gelman, Benjamin B, McArthur, Justin, McCutchan, Allen, Morgello, Susan, Simpson, David, Connor, James, Grant, Igor, Kallianpur, Asha

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The properties of ion-water clusters. I. The protonated 21-water cluster von Iyengar, Srinivasan S., Petersen, Matt K., Day, Tyler J. F., Burnham, Christian J., Teige, Virginia E., Voth, Gregory A.

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Increased cell-free mitochondrial DNA is a marker of ongoing inflammation and better neurocognitive function in virologically suppressed HIV-infected individuals von Pérez-Santiago, Josué, De Oliveira, Michelli F., Var, Susanna R., Day, Tyler R. C., Woods, Steven P., Gianella, Sara, Mehta, Sanjay R.

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Subtype associations with HIV-associated neurocognitive disorder in China von Day, Tyler R. C., Smith, Davey M., Heaton, Robert K., Franklin, Donald, Tilghman, Myers W., Letendre, Scott, Jin, Hua, Wu, Zunyou, Shi, Chuan, Yu, Xin, Pérez-Santiago, Josué

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A second generation multistate empirical valence bond model for proton transport in aqueous systems von Day, Tyler J. F., Soudackov, Alexander V., Čuma, Martin, Schmitt, Udo W., Voth, Gregory A.

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The properties of ion-water clusters. II. Solvation structures of Na + , Cl − , and H + clusters as a function of temperature von Burnham, Christian J., Petersen, Matt K., Day, Tyler J. F., Iyengar, Srinivasan S., Voth, Gregory A.

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The Mechanism of Hydrated Proton Transport in Water von Day, Tyler J. F, Schmitt, Udo W, Voth, Gregory A

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Ab initio structure prediction of the antibody hypervariable H3 loop von Zhu, Kai, Day, Tyler

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On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study von Iyengar, Srinivasan S., Day, Tyler J.F., Voth, Gregory A.

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Ion solvation dynamics in water–methanol and water– dimethylsulfoxide mixtures von Day, Tyler J. F., Patey, G. N.

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Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling von Sindhikara, Dan, Spronk, Steven A, Day, Tyler, Borrelli, Ken, Cheney, Daniel L, Posy, Shana L

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