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1
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Structure-Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Dickson, Callum J ; Hornak, Viktor ; Pearlstein, Robert A ; Duca, Jose S

Journal of the American Chemical Society, 11 January 2017, Vol.139(1), pp.442-452 [Peer Reviewed Journal]

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2
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Calculating Kinetic Rates and Membrane Permeability from Biased Simulations

Badaoui, Magd ; Kells, Adam ; Molteni, Carla ; Dickson, Callum J ; Hornak, Viktor ; Rosta, Edina

The journal of physical chemistry. B, 13 December 2018, Vol.122(49), pp.11571-11578 [Peer Reviewed Journal]

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3
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The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

Layten, Melinda ; Hornak, Viktor ; Simmerling, Carlos

Journal of the American Chemical Society, 18 October 2006, Vol.128(41), pp.13360-1 [Peer Reviewed Journal]

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4
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HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

Hornak, Viktor ; Okur, Asim ; Rizzo, Robert C ; Simmerling, Carlos

Journal of the American Chemical Society, 08 March 2006, Vol.128(9), pp.2812-3 [Peer Reviewed Journal]

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5
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Role of group-conserved residues in the helical core of beta2-adrenergic receptor

Chelikani, Prashen ; Hornak, Viktor ; Eilers, Markus ; Reeves, Phillip J ; Smith, Steven O ; Rajbhandary, Uttam L ; Khorana, H Gobind

Proceedings of the National Academy of Sciences of the United States of America, 24 April 2007, Vol.104(17), pp.7027-32 [Peer Reviewed Journal]

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6
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HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

Hornak, Viktor ; Okur, Asim ; Rizzo, Robert C ; Simmerling, Carlos

Proceedings of the National Academy of Sciences of the United States of America, 24 January 2006, Vol.103(4), pp.915-20 [Peer Reviewed Journal]

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7
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Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding

Dickson, Callum J ; Hornak, Viktor ; Velez-Vega, Camilo ; Mckay, Daniel J J ; Reilly, John ; Sandham, David A ; Shaw, Duncan ; Fairhurst, Robin A ; Charlton, Steven J ; Sykes, David A ; Pearlstein, Robert A ; Duca, Jose S

Journal of medicinal chemistry, 23 June 2016, Vol.59(12), pp.5780-9 [Peer Reviewed Journal]

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8
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Comparison of random forest and Pipeline Pilot Naïve Bayes in prospective QSAR predictions

Chen, Bin ; Sheridan, Robert P ; Hornak, Viktor ; Voigt, Johannes H

Journal of chemical information and modeling, 26 March 2012, Vol.52(3), pp.792-803 [Peer Reviewed Journal]

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9
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Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators

Pearlstein, Robert A ; Dickson, Callum J ; Hornak, Viktor

BBA - Biomembranes, February 2017, Vol.1859(2), pp.177-194 [Peer Reviewed Journal]

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10
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Light Activation of Rhodopsin: Insights from Molecular Dynamics Simulations Guided by Solid-State NMR Distance Restraints

Hornak, Viktor ; Ahuja, Shivani ; Eilers, Markus ; Goncalves, Joseph A ; Sheves, Mordechai ; Reeves, Philip J ; Smith, Steven O

Journal of Molecular Biology, 26 February 2010, Vol.396(3), pp.510-527 [Peer Reviewed Journal]

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11
Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches
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Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches

Cheng, Xiaolin ; Hornak, Viktor ; Simmerling, Carlos

The Journal of Physical Chemistry B, 01/2004, Vol.108(1), pp.426-437 [Peer Reviewed Journal]

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12
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Dynamic behavior of DNA base pairs containing 8-oxoguanine

Cheng, Xiaolin ; Kelso, Catherine ; Hornak, Viktor ; De Los Santos, Carlos ; Grollman, Arthur P ; Simmerling, Carlos

Journal of the American Chemical Society, 12 October 2005, Vol.127(40), pp.13906-18 [Peer Reviewed Journal]

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13
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Modified replica exchange simulation methods for local structure refinement

Cheng, Xiaolin ; Cui, Guanglei ; Hornak, Viktor ; Simmerling, Carlos

The journal of physical chemistry. B, 28 April 2005, Vol.109(16), pp.8220-30 [Peer Reviewed Journal]

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14
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Folding Cooperativity in a Three-stranded β-Sheet Model

Roe, Daniel R ; Hornak, Viktor ; Simmerling, Carlos

Journal of Molecular Biology, 2005, Vol.352(2), pp.370-381 [Peer Reviewed Journal]

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15
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Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction

Wickstrom, Lauren ; Bi, Yuan ; Hornak, Viktor ; Raleigh, Daniel P ; Simmerling, Carlos

Biochemistry, 27 March 2007, Vol.46(12), pp.3624-34 [Peer Reviewed Journal]

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16
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Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

Roe, Daniel R ; Okur, Asim ; Wickstrom, Lauren ; Hornak, Viktor ; Simmerling, Carlos

The journal of physical chemistry. B, 22 February 2007, Vol.111(7), pp.1846-57 [Peer Reviewed Journal]

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17
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Comparison of class A and D G protein-coupled receptors: common features in structure and activation

Eilers, Markus ; Hornak, Viktor ; Smith, Steven O ; Konopka, James B

Biochemistry, 28 June 2005, Vol.44(25), pp.8959-75 [Peer Reviewed Journal]

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18
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The design and synthesis of potent, selective benzodiazepine sulfonamide bombesin receptor subtype 3 (BRS-3) agonists with an increased barrier of atropisomerization

Chobanian, Harry R ; Guo, Yan ; Liu, Ping ; Lanza, Thomas J ; Chioda, Marc ; Chang, Linda ; Kelly, Theresa M ; Kan, Yanqing ; Palyha, Oksana ; Guan, Xiao-Ming ; Marsh, Donald J ; Metzger, Joseph M ; Raustad, Katie ; Wang, Sheng-Ping ; Strack, Alison M ; Gorski, Judith N ; Miller, Randy ; Pang, Jianmei ; Lyons, Kathy ; Dragovic

Bioorganic & medicinal chemistry, 01 May 2012, Vol.20(9), pp.2845-9 [Peer Reviewed Journal]

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19
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Structure–activity relationship of cytochrome bc1 reductase inhibitor broad spectrum antifungal ilicicolin H

Singh, Sheo B ; Liu, Weiguo ; Li, Xiaohua ; Chen, Tom ; Shafiee, Ali ; Dreikorn, Sarah ; Hornak, Viktor ; Meinz, Maria ; Onishi, Janet C

Bioorganic & Medicinal Chemistry Letters, 15 May 2013, Vol.23(10), pp.3018-3022 [Peer Reviewed Journal]

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20
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Crystallographic Structure of the K Intermediate of Bacteriorhodopsin: Conservation of Free Energy after Photoisomerization of the Retinal

Schobert, Brigitte ; Cupp-Vickery, Jill ; Hornak, Viktor ; Smith, Steven O ; Lanyi, Janos K

Journal of Molecular Biology, 2002, Vol.321(4), pp.715-726 [Peer Reviewed Journal]

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21
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Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase

Song, Kun ; Hornak, Viktor ; De Los Santos, Carlos ; Grollman, Arthur P ; Simmerling, Carlos

Biochemistry, 12 September 2006, Vol.45(36), pp.10886-94 [Peer Reviewed Journal]

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22
Dynamics of Rnase Sa :  A Simulation Perspective Complementary to NMR/X-ray
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Dynamics of Rnase Sa :  A Simulation Perspective Complementary to NMR/X-ray

Dvorsky, Radovan ; Hornak, Viktor ; Sevcik, Jozef ; Tyrrell, Graham P. ; Caves, Leo S. D. ; Verma, Chandra S.

The Journal of Physical Chemistry B, 06/2002, Vol.106(23), pp.6038-6048 [Peer Reviewed Journal]

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23
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Location of Trp265 in Metarhodopsin II: Implications for the Activation Mechanism of the Visual Receptor Rhodopsin

Crocker, Evan ; Eilers, Markus ; Ahuja, Shivani ; Hornak, Viktor ; Hirshfeld, Amiram ; Sheves, Mordechai ; Smith, Steven O

Journal of Molecular Biology, 2006, Vol.357(1), pp.163-172 [Peer Reviewed Journal]

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24
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The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure

Wickstrom, Lauren ; Okur, Asim ; Song, Kun ; Hornak, Viktor ; Raleigh, Daniel P ; Simmerling, Carlos L

Journal of Molecular Biology, 2006, Vol.360(5), pp.1094-1107 [Peer Reviewed Journal]

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25
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Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin

Crocker, Evan ; Eilers, Markus ; Ahuja, Shivani ; Hornak, Viktor ; Hirshfeld, Amiram ; Sheves, Mordechai ; Smith, Steven O

Journal of molecular biology, 17 March 2006, Vol.357(1), pp.163-72 [Peer Reviewed Journal]

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26
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Targeting structural flexibility in HIV-1 protease inhibitor binding

Hornak, Viktor ; Simmerling, Carlos

Drug Discovery Today, 2007, Vol.12(3), pp.132-138 [Peer Reviewed Journal]

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27
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Antifungal spectrum, in vivo efficacy, and structure-activity relationship of ilicicolin h

Singh, Sheo B ; Liu, Weiguo ; Li, Xiaohua ; Chen, Tom ; Shafiee, Ali ; Card, Deborah ; Abruzzo, George ; Flattery, Amy ; Gill, Charles ; Thompson, John R ; Rosenbach, Mark ; Dreikorn, Sarah ; Hornak, Viktor ; Meinz, Maria ; Kurtz, Myra ; Kelly, Rosemarie ; Onishi, Janet C

ACS medicinal chemistry letters, 11 October 2012, Vol.3(10), pp.814-7 [Peer Reviewed Journal]

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28
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Location of the retinal chromophore in the activated state of rhodopsin*

Ahuja, Shivani ; Crocker, Evan ; Eilers, Markus ; Hornak, Viktor ; Hirshfeld, Amiram ; Ziliox, Martine ; Syrett, Natalie ; Reeves, Philip J ; Khorana, H Gobind ; Sheves, Mordechai ; Smith, Steven O

The Journal of biological chemistry, 10 April 2009, Vol.284(15), pp.10190-201 [Peer Reviewed Journal]

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29
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Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations

Hornak, Viktor ; Simmerling, Carlos

Journal of Molecular Graphics and Modelling, 2004, Vol.22(5), pp.405-413 [Peer Reviewed Journal]

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30
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Generation of accurate protein loop conformations through low‐barrier molecular dynamics

Hornak, Viktor ; Simmerling, Carlos

Proteins: Structure, Function, and Bioinformatics, 01 June 2003, Vol.51(4), pp.577-590 [Peer Reviewed Journal]

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31
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Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening

Chen, Lieyang ; Cruz, Anthony ; Ramsey, Steven ; Dickson, Callum J ; Duca, Jose S ; Hornak, Viktor ; Koes, David R ; Kurtzman, Tom Zhang, Yang (editor)

PLoS ONE, 2019, Vol.14(8) [Peer Reviewed Journal]

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32
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Discovery of phenyl acetamides as potent and selective GPR119 agonists

Zhu, Cheng ; Wang, Liping ; Zhu, Yuping ; Guo, Zack Zhiqiang ; Liu, Ping ; Hu, Zhiyong ; Szewczyk, Jason W ; Kang, Ling ; Chicchi, Gary ; Ehrhardt, Anka ; Woods, Andrea ; Seo, Toru ; Woods, Morgan ; van Heek, Margaret ; Dingley, Karen H ; Pang, Jianmei ; Salituro, Gino M ; Powell, Joyce ; Terebetski, Jenna L ; Hornak, Viktor

Bioorganic & Medicinal Chemistry Letters, 01 March 2017, Vol.27(5), pp.1124-1128 [Peer Reviewed Journal]

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33
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Discovery of 8-Amino-imidazo[1,5- a ]pyrazines as Reversible BTK Inhibitors for the Treatment of Rheumatoid Arthritis

Liu, Jian ; Guiadeen, Deodial ; Krikorian, Arto ; Gao, Xiaolei ; Wang, James ; Boga, Sobhana Babu ; Alhassan, Abdul-Basit ; Yu, Younong ; Vaccaro, Henry ; Liu, Shilan ; Yang, Chundao ; Wu, Hao ; Cooper, Alan ; de Man, Jos ; Kaptein, Allard ; Maloney, Kevin ; Hornak, Viktor ; Gao, Ying-Duo ; Fischmann, Thierry O ; Raaijmakers, Hans ; Vu-Pham, Diep ; Presland, Jeremy ; Mansueto, My ; Xu, Zangwei ; Leccese, Erica ; Zhang-Hoover, Jie ; Knemeyer, Ian ; Garlisi, Charles G ; Bays, Nathan ; Stivers, Peter ; Brandish, Philip E ; Hicks, Alexandra ; Kim, Ronald ; Kozlowski, Joseph A Argonne National Lab. (Anl), Argonne, Il (United States). Advanced Photon Source (APS) (Corporate Author)

ACS Medicinal Chemistry Letters, 11 February 2016, Vol.7(2) [Peer Reviewed Journal]

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34
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Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

Okur, Asim ; Strockbine, Bentley ; Hornak, Viktor ; Simmerling, Carlos Frenking, Gernot ; Jorgensen, William L.

Journal of Computational Chemistry, 15 January 2003, Vol.24(1), pp.21-31 [Peer Reviewed Journal]

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35
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Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules

Dickson, Callum J ; Hornak, Viktor ; Bednarczyk, Dallas ; Duca, Jose S

Journal of chemical information and modeling, 28 January 2019, Vol.59(1), pp.236-244 [Peer Reviewed Journal]

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36
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Molecular mechanics parameters for the FapydG DNA lesion

Song, Kun ; Hornak, Viktor ; De Los Santos, Carlos ; Grollman, Arthur P. ; Simmerling, Carlos

Journal of Computational Chemistry, January 2008, Vol.29(1), pp.17-23 [Peer Reviewed Journal]

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