The effect of long-range electrostatic interactions in simulations of macromolecular crystals : a comparison of the Ewald and truncated list methods von YORK, D. M, DARDEN, T. A, PEDERSEN, L. G

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Atomic-Level Accuracy in Simulations of Large Protein Crystals von York, Darrin M., Wlodawer, Alexander, Pedersen, Lee G., Darden, Tom A.

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Explicit Water Near the Catalytic I Helix Thr in the Predicted Solution Structure of CYP2A4 von Gorokhov, Anna, Negishi, Masahiko, Johnson, Eric F., Pedersen, Lars C., Perera, Lalith, Darden, Tom A., Pedersen, Lee G.

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Adventures in improving the scaling and accuracy of a parallel molecular dynamics program von Crowley, Michael F, Darden, Tom A, Cheatham, Thomas EIII, Deerfield, David WII

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ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions von Procacci, Piero, Darden, Tom A., Paci, Emanuele, Marchi, Massimo

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Algorithms for Molecular Dynamics Simulations von Hedman, Fredrik

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Algorithms for Molecular Dynamics Simulations von Hedman Fredrik 1962- , Stockholms universitet, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Hedman Fredrik 1962-, Stockholm University, Department of Physical Chemistry, Inorganic Chemistry and Structural Chemistry

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Molecular Modeling Studies Suggest That Zinc Ions Inhibit HIV-1 Protease by Binding at Catalytic Aspartates von York, Darrin M., Darden, Tom A., Pedersen, Lee G., Anderson, Marshall W.

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Making optimal use of empirical energy functions: Force-field parameterization in crystal space von Krieger, Elmar, Darden, Tom, Nabuurs, Sander B., Finkelstein, Alexei, Vriend, Gert

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The Amber biomolecular simulation programs von Case, David A., Cheatham III, Thomas E., Darden, Tom, Gohlke, Holger, Luo, Ray, Merz Jr, Kenneth M., Onufriev, Alexey, Simmerling, Carlos, Wang, Bing, Woods, Robert J.

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Gaussian induced dipole polarization model von Elking, Dennis, Darden, Tom, Woods, Robert J.

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Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions von Toukmaji, Abdulnour, Sagui, Celeste, Board, John, Darden, Tom

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Signalling males increase or decrease their calling effort according to the proximity of rivals in a wild cricket von Wilde, Joe A., Rodríguez-Muñoz, Rolando, Darden, Safi K., Tregenza, Tom, Fawcett, Tim W.

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New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations von Darden, Tom, Perera, Lalith, Li, Leping, Pedersen, Lee

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A smooth particle mesh Ewald method von Essmann, Ulrich, Perera, Lalith, Berkowitz, Max L., Darden, Tom, Lee, Hsing, Pedersen, Lee G.

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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems von Darden, Tom, York, Darrin, Pedersen, Lee

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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop von Adams, Paul D., Aertgeerts, Kathleen, Bauer, Cary, Bell, Jeffrey A., Berman, Helen M., Bhat, Talapady N., Blaney, Jeff M., Bolton, Evan, Bricogne, Gerard, Brown, David, Burley, Stephen K., Case, David A., Clark, Kirk L., Darden, Tom, Emsley, Paul, Feher, Victoria A., Feng, Zukang, Groom, Colin R., Harris, Seth F., Hendle, Jorg, Holder, Thomas, Joachimiak, Andrzej, Kleywegt, Gerard J., Krojer, Tobias, Marcotrigiano, Joseph, Mark, Alan E., Markley, John L., Miller, Matthew, Minor, Wladek, Montelione, Gaetano T., Murshudov, Garib, Nakagawa, Atsushi, Nakamura, Haruki, Nicholls, Anthony, Nicklaus, Marc, Nolte, Robert T., Padyana, Anil K., Peishoff, Catherine E., Pieniazek, Susan, Read, Randy J., Shao, Chenghua, Sheriff, Steven, Smart, Oliver, Soisson, Stephen, Spurlino, John, Stouch, Terry, Svobodova, Radka, Tempel, Wolfram, Terwilliger, Thomas C., Tronrud, Dale, Velankar, Sameer, Ward, Suzanna C., Warren, Gregory L., Westbrook, John D., Williams, Pamela, Yang, Huanwang, Young, Jasmine

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Ionic charging free energies: Spherical versus periodic boundary conditions von Darden, Tom, Pearlman, David, Pedersen, Lee G.

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Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg²⁺-coordinating Thr of regulatory GTPases von Zurita, Adolfo, Zhang, Yinghao, Pedersen, Lee, Darden, Tom, Birnbaumer, Lutz

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Structure and Dynamics of Zymogen Human Blood Coagulation Factor X von Venkateswarlu, Divi, Perera, Lalith, Darden, Tom, Pedersen, Lee G.

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