Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water (English)
- New search for: Li, Pengfei
- New search for: Song, Lin Frank
- New search for: Merz, Kenneth M.
- New search for: Li, Pengfei
- New search for: Song, Lin Frank
- New search for: Merz, Kenneth M.
In:
The Journal of Physical Chemistry B
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119
, 3
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883-895
;
2015
- Article (Journal) / Electronic Resource
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Title:Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit Water
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Additional title:J. Phys. Chem. B
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Contributors:
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Published in:The Journal of Physical Chemistry B ; 119, 3 ; 883-895
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Publisher:
- New search for: American Chemical Society
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Publication date:2015-01-22
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ISSN:
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Coden:
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DOI:
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Type of media:Article (Journal)
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Type of material:Electronic Resource
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Language:English
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Source:
Table of contents – Volume 119, Issue 3
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 621
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Tribute to William L. JorgensenGao, Jiali / Orozco, Modesto / Peishoff, Catherine E. et al. | 2015
- 624
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Autobiography of William L. Jorgensen: Scientific History and RecollectionsJorgensen, William L. et al. | 2015
- 633
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Group Members of William L. Jorgensen (1975–2014)| 2015
- 635
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Abbreviated Curriculum Vitae of William L. Jorgensen| 2015
- 637
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Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude OscillatorPatel, Dhilon S. / He, Xibing / MacKerell, Alexander D. et al. | 2015
- 653
-
A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar CouplingsCamilloni, Carlo / Vendruscolo, Michele et al. | 2015
- 662
-
Computer Simulation Studies of Aβ37–42 Aggregation Thermodynamics and Kinetics in Water and Salt SolutionYang, Y. Isaac / Gao, Yi Qin et al. | 2015
- 671
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Atomic Picture of Ligand Migration in Toluene 4‑MonooxygenaseHosseini, Ali / Brouk, Moran / Lucas, Maria Fatima / Glaser, Fabian / Fishman, Ayelet / Guallar, Victor et al. | 2015
- 679
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Solvent-Induced O–H Vibration Red-Shifts of Oxygen-Acids in Hydrogen-Bonded O–H···Base ComplexesKeinan, Sharon / Pines, Dina / Kiefer, Philip M. / Hynes, James T. / Pines, Ehud et al. | 2015
- 693
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Hydrogen-Tunneling in Biologically Relevant Small Molecules: The Rotamerizations of α‑Ketocarboxylic AcidsGerbig, Dennis / Schreiner, Peter R. et al. | 2015
- 704
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Direct QM/MM Excited-State Dynamics of Retinal Protonated Schiff Base in Isolation and Methanol SolutionPunwong, Chutintorn / Owens, Jane / Martínez, Todd J. et al. | 2015
- 715
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Steered Quantum Dynamics for Energy MinimizationSoley, Micheline / Markmann, Andreas / Batista, Victor S. et al. | 2015
- 728
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Intricate Internal Rotation Surface and Fundamental Infrared Transitions of the n‑Propyl RadicalLi, Chenyang / Agarwal, Jay / Wu, Chia-Hua / Allen, Wesley D. / Schaefer, Henry F. et al. | 2015
- 736
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A Time-Independent Free Energy Estimator for MetadynamicsTiwary, Pratyush / Parrinello, Michele et al. | 2015
- 743
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Ionic Liquid Effects on Nucleophilic Aromatic Substitution Reactions from QM/MM SimulationsAllen, Caley / McCann, Billy W. / Acevedo, Orlando et al. | 2015
- 753
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Challenge of Representing Entropy at Different Levels of Resolution in Molecular SimulationHuang, Wei / van Gunsteren, Wilfred F. et al. | 2015
- 764
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Interactions of Lipids and Detergents with a Viral Ion Channel Protein: Molecular Dynamics Simulation StudiesRouse, Sarah L. / Sansom, Mark S. P. et al. | 2015
- 773
-
Binding Site Preorganization and Ligand Discrimination in the Purine RiboswitchSund, Johan / Lind, Christoffer / Åqvist, Johan et al. | 2015
- 783
-
Hydrogen-Atom Abstraction from a Model Amino Acid: Dependence on the Attacking RadicalAmos, Ruth I. J. / Chan, Bun / Easton, Christopher J. / Radom, Leo et al. | 2015
- 789
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Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen InversionPalermo, Giulia / Campomanes, Pablo / Cavalli, Andrea / Rothlisberger, Ursula / De Vivo, Marco et al. | 2015
- 802
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Solvent Effects on Isotope Effects: Methyl Cation as a Model SystemWilson, Philippe B. / Weaver, Paul J. / Greig, Ian R. / Williams, Ian H. et al. | 2015
- 810
-
Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy CalculationsLundborg, Magnus / Lindahl, Erik et al. | 2015
- 824
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Docking and Free Energy Perturbation Studies of Ligand Binding in the Kappa Opioid ReceptorGoldfeld, Dahlia A. / Murphy, Robert / Kim, Byungchan / Wang, Lingle / Beuming, Thijs / Abel, Robert / Friesner, Richard A. et al. | 2015
- 836
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Optimizing Potentials for a Liquid Mixture: A New Force Field for a tert-Butanol and Water SolutionDi Pierro, Michele / Mugnai, Mauro L. / Elber, Ron et al. | 2015
- 850
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Theoretical Insight into the Relationship between the Structures of Antimicrobial Peptides and Their Actions on Bacterial MembranesChen, Licui / Li, Xiaoxu / Gao, Lianghui / Fang, Weihai et al. | 2015
- 861
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Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free EnergiesKim, M. Olivia / Blachly, Patrick G. / Kaus, Joseph W. / McCammon, J. Andrew et al. | 2015
- 873
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Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O‑MethyltransferaseGarcía-Meseguer, Rafael / Zinovjev, Kirill / Roca, Maite / Ruiz-Pernía, Javier J. / Tuñón, Iñaki et al. | 2015
- 883
-
Parameterization of Highly Charged Metal Ions Using the 12-6‑4 LJ-Type Nonbonded Model in Explicit WaterLi, Pengfei / Song, Lin Frank / Merz, Kenneth M. et al. | 2015
- 896
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Disordered Structural Ensembles of Vasopressin and Oxytocin and Their MutantsYedvabny, Eugene / Nerenberg, Paul S. / So, Clare / Head-Gordon, Teresa et al. | 2015
- 906
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Free Energy Simulations of Active-Site Mutants of Dihydrofolate ReductaseDoron, Dvir / Stojković, Vanja / Gakhar, Lokesh / Vardi-Kilshtain, Alexandra / Kohen, Amnon / Major, Dan Thomas et al. | 2015
- 917
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Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV‑1 RTKrzemińska, Agnieszka / Paneth, Piotr / Moliner, Vicent / Świderek, Katarzyna et al. | 2015
- 928
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Photoinduced Intramolecular Charge Transfer in an Electronically Modified Flavin Derivative: RoseoflavinKarasulu, Bora / Thiel, Walter et al. | 2015
- 944
-
Role of Hydrophilicity and Length of Diblock Arms for Determining Star Polymer Physical PropertiesFelberg, Lisa E. / Brookes, David H. / Head-Gordon, Teresa / Rice, Julia E. / Swope, William C. et al. | 2015
- 958
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Electronic Absorption Spectra and Solvatochromic Shifts by the Vertical Excitation Model: Solvated Clusters and Molecular Dynamics SamplingMarenich, Aleksandr V. / Cramer, Christopher J. / Truhlar, Donald G. et al. | 2015
- 968
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Rapid Alchemical Free Energy Calculation Employing a Generalized Born Implicit Solvent ModelOstermeir, Katja / Zacharias, Martin et al. | 2015
- 976
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Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV ProteaseDeng, Nanjie / Forli, Stefano / He, Peng / Perryman, Alex / Wickstrom, Lauren / Vijayan, R. S. K. / Tiefenbrunn, Theresa / Stout, David / Gallicchio, Emilio / Olson, Arthur J. et al. | 2015
- 989
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Evolution Alters the Enzymatic Reaction Coordinate of Dihydrofolate ReductaseMasterson, Jean E. / Schwartz, Steven D. et al. | 2015
- 997
-
Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein–Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza NeuraminidaseWoods, Christopher J. / Shaw, Katherine E. / Mulholland, Adrian J. et al. | 2015
- 1002
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Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3KαGkeka, Paraskevi / Papafotika, Alexandra / Christoforidis, Savvas / Cournia, Zoe et al. | 2015
- 1017
-
Direct Validation of the Single Step Classical to Quantum Free Energy PerturbationCave-Ayland, Christopher / Skylaris, Chris-Kriton / Essex, Jonathan W. et al. | 2015
- 1026
-
Multi-Conformer Ensemble Docking to Difficult Protein TargetsEllingson, Sally R. / Miao, Yinglong / Baudry, Jerome / Smith, Jeremy C. et al. | 2015
- 1035
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Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SBZhou, Chen-Yang / Jiang, Fan / Wu, Yun-Dong et al. | 2015
- 1048
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Biophysical Characteristics of Cholera Toxin and Escherichia coli Heat-Labile Enterotoxin Structure and Chemistry Lead to Differential ToxicityCraft, John W. / Shen, Tsai-wei / Brier, Lindsey M. / Briggs, James M. et al. | 2015
- 1062
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Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological ApplicationsLu, Xiya / Gaus, Michael / Elstner, Marcus / Cui, Qiang et al. | 2015
- 1083
-
Pharmacophore-Based Similarity Scoring for DOCKJiang, Lingling / Rizzo, Robert C. et al. | 2015
- 1103
-
Enzymatic Minimum Free Energy Path Calculations Using Swarms of TrajectoriesSanchez-Martinez, Melchor / Field, Martin / Crehuet, Ramon et al. | 2015
- 1114
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Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics SimulationsAllnér, Olof / Foloppe, Nicolas / Nilsson, Lennart et al. | 2015
- 1129
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The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To AskComer, Jeffrey / Gumbart, James C. / Hénin, Jérôme / Lelièvre, Tony / Pohorille, Andrew / Chipot, Christophe et al. | 2015
- 1152
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Aqueous Transition-Metal Cations as Impurities in a Wide Gap Oxide: The Cu2+/Cu+ and Ag2+/Ag+ Redox Couples RevisitedLiu, Xiandong / Cheng, Jun / Sprik, Michiel et al. | 2015
- 1164
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Assessing the Suitability of the Multilevel Strategy for the Conformational Analysis of Small LigandsJuárez-Jiménez, Jordi / Barril, Xavier / Orozco, Modesto / Pouplana, Ramon / Luque, F. Javier et al. | 2015
- 1173
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Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based InhibitorsGianti, Eleonora / Carnevale, Vincenzo / DeGrado, William F. / Klein, Michael L. / Fiorin, Giacomo et al. | 2015
- 1184
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Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair CarboxyphosphateKochanek, Sarah E. / Clymer, Traci M. / Pakkala, Venkata S. / Hebert, Sebastien P. / Reeping, Kyle / Firestine, Steven M. / Evanseck, Jeffrey D. et al. | 2015
- 1192
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Profiling Transition-State Configurations on the Trypanosoma cruzi trans-Sialidase Free-Energy Reaction SurfacesRogers, Ian L. / Naidoo, Kevin J. et al. | 2015
- 1202
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Can Gap Tuning Schemes of Long-Range Corrected Hybrid Functionals Improve the Description of Hyperpolarizabilities?Garza, Alejandro J. / Osman, Osman I. / Asiri, Abdullah M. / Scuseria, Gustavo E. et al. | 2015
- 1213
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Projected Hybrid Orbitals: A General QM/MM MethodWang, Yingjie / Gao, Jiali et al. | 2015
- 1225
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Why Bound Amantadine Fails to Inhibit Proton Conductance According to Simulations of the Drug-Resistant Influenza A M2 (S31N)Gleed, Mitchell L. / Busath, David D. et al. | 2015