Viktor Hornak: search on Z-Library

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1

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

Bussiere, Dirksen E., Xie, Lili, Srinivas, Honnappa, Shu, Wei, Burke, Ashley, Be, Celine, Zhao, Junping, Godbole, Adarsh, King, Dan, Karki, Rajeshri G., Hornak, Viktor, Xu, Fangmin, Cobb, Jennifer, Ca

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 8.84 MB

2020

2

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

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

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 420 KB

english, 2006

3

Calculating Kinetic Rates and Membrane Permeability from Biased Simulation

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

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 6.83 MB

english, 2018

4

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

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2016

Language:

english

File:

PDF, 2.64 MB

english, 2016

5

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.

Journal:

Journal of Physical Chemistry B

Year:

2002

Language:

english

File:

PDF, 655 KB

english, 2002

6

Comparison of Random Forest and Pipeline Pilot Naïve Bayes in Prospective QSAR Predictions

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

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 3.09 MB

english, 2012

7

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

Journal:

Year:

2006

Language:

english

File:

PDF, 470 KB

english, 2006

8

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.

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 778 KB

english, 2013

9

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

Okur, Asim, Wickstrom, Lauren, Layten, Melinda, Geney, Raphäel, Song, Kun, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 546 KB

english, 2006

10

Modified Replica Exchange Simulation Methods for Local Structure Refinement

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

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 789 KB

english, 2005

11

Reconciling the Solution and X-ray Structures of the Villin Headpiece Helical Subdomain: Molecular Dynamics Simulations and Double Mutant Cycles Reveal a Stabilizing Cation−π Interaction †

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

Journal:

Year:

2007

Language:

english

File:

PDF, 679 KB

english, 2007

12

Structure-based design and pre-clinical characterization of selective and orally bioavailable Factor XIa inhibitors: Demonstrating the power of an integrated S1 protease family approach.

Lorthiois, Edwige, Roache, James, Barnes-Seeman, David, Altmann, Eva, Hassiepen, Ulrich, Turner, Gordon, Duvadie, Rohit, Hornak, Viktor, Karki, Rajeshri G., Schiering, Nikolaus, Weihofen, Wilhelm A.,

Journal:

Journal of Medicinal Chemistry

Year:

2020

File:

PDF, 1.75 MB

2020

13

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.

Journal:

Year:

2005

Language:

english

File:

PDF, 1.02 MB

english, 2005

14

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

Viktor Hornak, Carlos Simmerling

Journal:

Journal of Molecular Graphics and Modelling

Year:

2004

Language:

english

File:

PDF, 353 KB

english, 2004

15

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

Cheng, Xiaolin, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 725 KB

english, 2004

16

Folding Cooperativity in a Three-stranded β-Sheet Model

Daniel R. Roe, Viktor Hornak, Carlos Simmerling

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 702 KB

english, 2005

17

The Open Structure of a Multi-Drug-Resistant HIV-1 Protease is Stabilized by Crystal Packing Contacts

Layten, Melinda, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 164 KB

english, 2006

18

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, Me

Journal:

ACS Medicinal Chemistry Letters

Year:

2012

Language:

english

File:

PDF, 844 KB

english, 2012

19

Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation

Ahuja, Shivani, Hornak, Viktor, Yan, Elsa C Y, Syrett, Natalie, Goncalves, Joseph A, Hirshfeld, Amiram, Ziliox, Martine, Sakmar, Thomas P, Sheves, Mordechai, Reeves, Philip J

Journal:

Nature Structural and Molecular Biology

Year:

2009

Language:

english

File:

PDF, 890 KB

english, 2009

20

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:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 677 KB

english, 2005

21

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

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

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 326 KB

english, 2002

22

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

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

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.13 MB

english, 2010

23

Using membrane partitioning simulations to predict permeability of forty-nine drug-like molecules

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

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 828 KB

english, 2018

24

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

Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 303 KB

english, 2003

25

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 695 KB

english, 2006

26

Targeting structural flexibility in HIV-1 protease inhibitor binding

Viktor Hornak, Carlos Simmerling

Journal:

Drug Discovery Today

Year:

2007

Language:

english

File:

PDF, 511 KB

english, 2007

27

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

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

Journal:

Journal of the American Chemical Society

Year:

2017

Language:

english

File:

PDF, 1.10 MB

english, 2017

28

Molecular mechanics parameters for the FapydG DNA lesion

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

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 377 KB

english, 2008

29

Structure of a Transient Intermediate for GTP Hydrolysis by Ras

Bradley Ford, Viktor Hornak, Holly Kleinman, Nicolas Nassar

Journal:

Year:

2006

Language:

english

File:

PDF, 519 KB

english, 2006

30

Author Correction: Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

Bussiere, Dirksen E., Xie, Lili, Srinivas, Honnappa, Shu, Wei, Burke, Ashley, Be, Celine, Zhao, Junping, Godbole, Adarsh, King, Dan, Karki, Rajeshri G., Hornak, Viktor, Xu, Fangmin, Cobb, Jennifer, Ca

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 491 KB

2020

31

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

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

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

32

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model

Geney, Raphaël, Layten, Melinda, Gomperts, Roberto, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2006

Language:

english

File:

PDF, 614 KB

english, 2006

33

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

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 235 KB

english, 2007

34

Generation of accurate protein loop conformations through low-barrier molecular dynamics

Viktor Hornak, Carlos Simmerling

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 461 KB

english, 2003

35

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:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 118 KB

english, 2006

36

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

Okur, Asim, Roe, Daniel R., Cui, Guanglei, Hornak, Viktor, Simmerling, Carlos

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 234 KB

english, 2007

37

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, Rober

Journal:

Journal of Medicinal Chemistry

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

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