1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations (Unknown)
- New search for: Dodda, Leela S.
- New search for: Vilseck, Jonah Z.
- New search for: Tirado-Rives, Julian
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https://orcid.org/0000-0001-7330-189X
- New search for: Jorgensen, William L.
- Further information on Jorgensen, William L.:
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https://orcid.org/0000-0002-3993-9520
- New search for: Dodda, Leela S.
- New search for: Vilseck, Jonah Z.
- New search for: Tirado-Rives, Julian
- Further information on Tirado-Rives, Julian:
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https://orcid.org/0000-0001-7330-189X
- New search for: Jorgensen, William L.
- Further information on Jorgensen, William L.:
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https://orcid.org/0000-0002-3993-9520
In:
The Journal of Physical Chemistry B
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121
, 15
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3864-3870
;
2017
- Article (Journal) / Electronic Resource
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Title:1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations
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Additional title:J. Phys. Chem. B
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Contributors:Dodda, Leela S. ( author ) / Vilseck, Jonah Z. ( author ) / Tirado-Rives, Julian ( author ) / Jorgensen, William L. ( author )
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Published in:The Journal of Physical Chemistry B ; 121, 15 ; 3864-3870
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Publisher:
- New search for: American Chemical Society
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Publication date:2017-04-20
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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:Unknown
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Source:
Table of contents – Volume 121, Issue 15
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.
- 3203
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Tribute to Klaus SchultenTajkhorshid, Emad / Chipot, Christophe et al. | 2017
- 3206
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Biography of Klaus SchultenAmaro, Rommie E. / Villa, Elizabeth / Luthey-Schulten, Zan et al. | 2017
- 3207
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Colleagues of Klaus SchultenSchulten, Klaus et al. | 2017
- 3209
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Abbreviated Curriculum Vitae of Klaus SchultenSchulten, Klaus et al. | 2017
- 3210
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Selected Publications of Klaus SchultenSchulten, Klaus et al. | 2017
- 3228
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Protein Arrangement Effects on the Exciton Dynamics in the PE555 ComplexChandrasekaran, Suryanarayanan / Pothula, Karunakar Reddy / Kleinekathöfer, Ulrich et al. | 2017
- 3237
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Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membranevan Eerden, Floris J. / van den Berg, Tom / Frederix, Pim W. J. M. / de Jong, Djurre H. / Periole, Xavier / Marrink, Siewert J. et al. | 2017
- 3250
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Primary Fibril Nucleation of Aggregation Prone Tau Fragments PHF6 and PHF6*Smit, Florent X. / Luiken, Jurriaan A. / Bolhuis, Peter G. et al. | 2017
- 3262
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Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics SimulationsGu, Ruo-Xu / Ingólfsson, Helgi I. / de Vries, Alex H. / Marrink, Siewert J. / Tieleman, D. Peter et al. | 2017
- 3276
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Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic ContactKachlishvili, Khatuna / Dave, Kapil / Gruebele, Martin / Scheraga, Harold A. / Maisuradze, Gia G. et al. | 2017
- 3285
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A Distal Disulfide Bridge in OXA‑1 β‑Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω LoopSimakov, Nikolay / Leonard, David A. / Smith, Jeremy C. / Wymore, Troy / Szarecka, Agnieszka et al. | 2017
- 3297
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Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP SynthasesZhou, Wenchang / Leone, Vanessa / Krah, Alexander / Faraldo-Gómez, José D. et al. | 2017
- 3308
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Mutations at the Qo Site of the Cytochrome b c 1 Complex Strongly Affect Oxygen BindingHusen, Peter / Solov’yov, Ilia A. et al. | 2017
- 3318
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Origin of pK a Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit WaterWu, Xiongwu / Lee, Juyong / Brooks, Bernard R. et al. | 2017
- 3331
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Dynamics of the Orientational Factor in Fluorescence Resonance Energy TransferHummer, Gerhard / Szabo, Attila et al. | 2017
- 3340
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Does Proton Conduction in the Voltage-Gated H+ Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues?van Keulen, Siri C. / Gianti, Eleonora / Carnevale, Vincenzo / Klein, Michael L. / Rothlisberger, Ursula / Delemotte, Lucie et al. | 2017
- 3352
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The Activation of c‑Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy LandscapeFajer, Mikolai / Meng, Yilin / Roux, Benoît et al. | 2017
- 3364
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Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein AssociationDomański, Jan / Hedger, George / Best, Robert B. / Stansfeld, Phillip J. / Sansom, Mark S. P. et al. | 2017
- 3376
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Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 TransporterSong, Hyun Deok / Zhu, Fangqiang et al. | 2017
- 3387
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Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by PhosphorylationBomblies, Rainer / Luitz, Manuel P. / Zacharias, Martin et al. | 2017
- 3394
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Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics SimulationsGe, Zhenpeng / Wang, Yi et al. | 2017
- 3403
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Classical and Quantum Shortcuts to Adiabaticity in a Tilted PistonPatra, Ayoti / Jarzynski, Christopher et al. | 2017
- 3412
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Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155–4Yang, Mingjun / Simon, Raphael / MacKerell, Alexander D. et al. | 2017
- 3424
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Direct Measurement of the Effect of Cholesterol and 6‑Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics SimulationsShrestha, Rebika / Anderson, Cari M. / Cardenas, Alfredo E. / Elber, Ron / Webb, Lauren J. et al. | 2017
- 3437
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Dependence of the Enzymatic Velocity on the Substrate Dissociation RateBerezhkovskii, Alexander M. / Szabo, Attila / Rotbart, T. / Urbakh, M. / Kolomeisky, Anatoly B. et al. | 2017
- 3443
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Lipid and Peptide Diffusion in Bilayers: The Saffman–Delbrück Model and Periodic Boundary ConditionsVenable, Richard M. / Ingólfsson, Helgi I. / Lerner, Michael G. / Perrin, B. Scott / Camley, Brian A. / Marrink, Siewert J. / Brown, Frank L. H. / Pastor, Richard W. et al. | 2017
- 3458
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Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free EnergiesGosink, Luke J. / Overall, Christopher C. / Reehl, Sarah M. / Whitney, Paul D. / Mobley, David L. / Baker, Nathan A. et al. | 2017
- 3473
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Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β ProteinsChen, Mingchen / Lin, Xingcheng / Lu, Wei / Onuchic, José N. / Wolynes, Peter G. et al. | 2017
- 3483
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Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular DetailsMassarczyk, M. / Rudack, T. / Schlitter, J. / Kuhne, J. / Kötting, C. / Gerwert, K. et al. | 2017
- 3493
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A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen–Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein–Ligand InteractionsSaltzberg, Daniel J. / Broughton, Howard B. / Pellarin, Riccardo / Chalmers, Michael J. / Espada, Alfonso / Dodge, Jeffrey A. / Pascal, Bruce D. / Griffin, Patrick R. / Humblet, Christine / Sali, Andrej et al. | 2017
- 3502
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Methodology for the Simulation of Molecular Motors at Different ScalesSingharoy, Abhishek / Chipot, Christophe et al. | 2017
- 3515
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Ripping RNA by Force Using Gaussian Network ModelsHyeon, Changbong / Thirumalai, D. et al. | 2017
- 3523
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Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid MembranesHerzog, Florian A. / Braun, Lukas / Schoen, Ingmar / Vogel, Viola et al. | 2017
- 3536
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Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β‑Hairpin Maquette Determined through Spectroscopy and SimulationHwang, Hyea / McCaslin, Tyler G. / Hazel, Anthony / Pagba, Cynthia V. / Nevin, Christina M. / Pavlova, Anna / Barry, Bridgette A. / Gumbart, James C. et al. | 2017
- 3546
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Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?Skolnick, Jeffrey / Zhou, Hongyi et al. | 2017
- 3555
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Nonpolar Solvation Free Energy from Proximal Distribution FunctionsOu, Shu-Ching / Drake, Justin A. / Pettitt, B. Montgomery et al. | 2017
- 3565
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Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics SimulationsHan, Weiwei / Zhu, Jingxuan / Wang, Song / Xu, Dong et al. | 2017
- 3574
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Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline LectinFritz, Matthew / Quinn, Caitlin M. / Wang, Mingzhang / Hou, Guangjin / Lu, Xingyu / Koharudin, Leonardus M. I. / Polenova, Tatyana / Gronenborn, Angela M. et al. | 2017
- 3586
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Molecular Details of the PH Domain of ACAP1BAR‑PH Protein Binding to PIP-Containing MembraneChan, Kevin Chun / Lu, Lanyuan / Sun, Fei / Fan, Jun et al. | 2017
- 3597
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SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine BindingVotapka, Lane W. / Jagger, Benjamin R. / Heyneman, Alexandra L. / Amaro, Rommie E. et al. | 2017
- 3607
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Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion ChannelsPohorille, Andrew / Wilson, Michael A. / Wei, Chenyu et al. | 2017
- 3620
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Mechanical Stability of a High-Affinity Toxin Anchor from the Pathogen Clostridium perfringensMilles, Lukas F. / Bayer, Edward A. / Nash, Michael A. / Gaub, Hermann E. et al. | 2017
- 3626
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Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ DynamicsHayes, Ryan L. / Armacost, Kira A. / Vilseck, Jonah Z. / Brooks, Charles L. et al. | 2017
- 3636
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The Multiple Roles of Waters in Protein SolvationHospital, Adam / Candotti, Michela / Gelpí, Josep Lluís / Orozco, Modesto et al. | 2017
- 3644
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What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT?Immadisetty, Kalyan / Hettige, Jeevapani / Moradi, Mahmoud et al. | 2017
- 3657
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Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium SymportersGur, Mert / Cheng, Mary Hongying / Zomot, Elia / Bahar, Ivet et al. | 2017
- 3667
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Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase ηUcisik, Melek N. / Hammes-Schiffer, Sharon et al. | 2017
- 3676
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Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force MethodLesage, Adrien / Lelièvre, Tony / Stoltz, Gabriel / Hénin, Jérôme et al. | 2017
- 3686
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Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer PopulationsOzgur, Beytullah / Ozdemir, E. Sila / Gursoy, Attila / Keskin, Ozlem et al. | 2017
- 3701
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The Q‑Cycle Mechanism of the bc 1 Complex: A Biologist’s Perspective on Atomistic StudiesCrofts, Antony R. / Rose, Stuart W. / Burton, Rodney L. / Desai, Amit V. / Kenis, Paul J. A. / Dikanov, Sergei A. et al. | 2017
- 3718
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CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various EnvironmentsQi, Yifei / Lee, Jumin / Singharoy, Abhishek / McGreevy, Ryan / Schulten, Klaus / Im, Wonpil et al. | 2017
- 3724
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Modulation of Molecular Flux Using a Graphene Nanopore CapacitorShankla, Manish / Aksimentiev, Aleksei et al. | 2017
- 3734
-
Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with UreaMiner, Jacob C. / García, Angel E. et al. | 2017
- 3747
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Quantitative Characterization of Domain Motions in Molecular MachinesMaji, Suvrajit / Shahoei, Rezvan / Schulten, Klaus / Frank, Joachim et al. | 2017
- 3757
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Graphene Nanopores for Electronic Recognition of DNA MethylationSarathy, Aditya / Qiu, Hu / Leburton, Jean-Pierre et al. | 2017
- 3764
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Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico SolventsVermaas, Josh V. / Pogorelov, Taras V. / Tajkhorshid, Emad et al. | 2017
- 3777
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Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription ElongationE, Chao / Duan, Baogen / Yu, Jin et al. | 2017
- 3787
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Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural ModelsHitchcock, Andrew / Hunter, C. Neil / Sener, Melih et al. | 2017
- 3798
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Long-Range Dispersion Effects on the Water/Vapor Interface Simulated Using the Most Common ModelsSega, Marcello / Dellago, Christoph et al. | 2017
- 3804
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Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion ChannelWood, Mona L. / Freites, J. Alfredo / Tombola, Francesco / Tobias, Douglas J. et al. | 2017
- 3813
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Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel MutantsEinav, Tal / Phillips, Rob et al. | 2017
- 3825
-
Relationship between Solvation Thermodynamics from IST and DFT PerspectivesLevy, Ronald M. / Cui, Di / Zhang, Bin W. / Matubayasi, Nobuyuki et al. | 2017
- 3842
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Photoactivation Intermediates of a G‑Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular SimulationKamiya, Motoshi / Hayashi, Shigehiko et al. | 2017
- 3853
-
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics SimulationsPerilla, Juan R. / Zhao, Gongpu / Lu, Manman / Ning, Jiying / Hou, Guangjin / Byeon, In-Ja L. / Gronenborn, Angela M. / Polenova, Tatyana / Zhang, Peijun et al. | 2017
- 3864
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1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase SimulationsDodda, Leela S. / Vilseck, Jonah Z. / Tirado-Rives, Julian / Jorgensen, William L. et al. | 2017
- 3871
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Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell SimulationsEarnest, Tyler M. / Watanabe, Reika / Stone, John E. / Mahamid, Julia / Baumeister, Wolfgang / Villa, Elizabeth / Luthey-Schulten, Zaida et al. | 2017
- 3882
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Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome DepletionBascom, Gavin D / Kim, Taejin / Schlick, Tamar et al. | 2017
- 3895
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Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated DerivativesPoblete, Horacio / Miranda-Carvajal, Ingrid / Comer, Jeffrey et al. | 2017