Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation (Unknown)
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https://orcid.org/0000-0002-9787-0066
- New search for: Ó Conchúir, Shane
- New search for: Thompson, Samuel
- New search for: Suresh, Pooja
- New search for: Lucas, James E.
- New search for: Heinonen, Markus
- New search for: Kortemme, Tanja
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https://orcid.org/0000-0002-8494-680X
- New search for: Barlow, Kyle A.
- Further information on Barlow, Kyle A.:
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https://orcid.org/0000-0002-9787-0066
- New search for: Ó Conchúir, Shane
- New search for: Thompson, Samuel
- New search for: Suresh, Pooja
- New search for: Lucas, James E.
- New search for: Heinonen, Markus
- New search for: Kortemme, Tanja
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https://orcid.org/0000-0002-8494-680X
In:
The Journal of Physical Chemistry B
;
122
, 21
;
5389-5399
;
2018
- Article (Journal) / Electronic Resource
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Title:Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation
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Additional title:J. Phys. Chem. B
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Contributors:Barlow, Kyle A. ( author ) / Ó Conchúir, Shane ( author ) / Thompson, Samuel ( author ) / Suresh, Pooja ( author ) / Lucas, James E. ( author ) / Heinonen, Markus ( author ) / Kortemme, Tanja ( author )
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Published in:The Journal of Physical Chemistry B ; 122, 21 ; 5389-5399
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Publisher:
- New search for: American Chemical Society
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Publication date:2018-05-31
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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 122, Issue 21
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.
- 5261
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Tribute to Ken A. DillHribar-Lee, Barbara / Seok, Chaok / Coutsias, Evangelos / Lukšič, Miha et al. | 2018
- 5263
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Autobiography of Ken A. DillDill, Ken A. et al. | 2018
- 5267
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Colleagues of Ken A. DillDill, Ken A. et al. | 2018
- 5269
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Selected Publications of Ken A. DillDill, Ken A. et al. | 2018
- 5278
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Size-Dependent Relationships between Protein Stability and Thermal Unfolding Temperature Have Important Implications for Analysis of Protein Energetics and High-Throughput Assays of Protein–Ligand InteractionsWatson, Matthew D. / Monroe, Jeremy / Raleigh, Daniel P. et al. | 2018
- 5286
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Spatiotemporal Organization of Catalysts Driven by Enhanced DiffusionWeistuch, C. / Pressé, S. et al. | 2018
- 5291
-
Transfer Learning from Markov Models Leads to Efficient Sampling of Related SystemsSultan, Mohammad M. / Pande, Vijay S. et al. | 2018
- 5300
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Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp EliminasesBelsare, Saurabh / Pattni, Viren / Heyden, Matthias / Head-Gordon, Teresa et al. | 2018
- 5308
-
Molecular Dynamics and Neutron Scattering Studies of Mixed Solutions of Caffeine and Pyridine in WaterTavagnacco, Letizia / Mason, Philip E. / Neilson, George W. / Saboungi, Marie-Louise / Cesàro, Attilio / Brady, John W. et al. | 2018
- 5316
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Conformational Dynamics of Matrix Metalloproteinase-1·Triple-Helical Peptide ComplexesKarabencheva-Christova, Tatyana G. / Christov, Christo Z. / Fields, Gregg B. et al. | 2018
- 5327
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Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop TemplatesXu, Xiaojun / Chen, Shi-Jie et al. | 2018
- 5336
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Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine TransporterCheng, Mary Hongying / Kaya, Cihan / Bahar, Ivet et al. | 2018
- 5347
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RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network ModelKaynak, Burak T. / Findik, Doga / Doruker, Pemra et al. | 2018
- 5356
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Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star PolymersCarr, Amber C. / Piunova, Victoria A. / Maarof, Hasmerya / Rice, Julia E. / Swope, William C. et al. | 2018
- 5368
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Path to the Desensitized State of Ligand-Gated Ion Channels: Why Are Inhibitory and Excitatory Receptors Different?Cantor, Robert S. et al. | 2018
- 5375
-
Influence of Intermolecular Coupling on the Vibrational Spectrum of WaterMatt, Sarah M. / Ben-Amotz, Dor et al. | 2018
- 5381
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DNA–Polyelectrolyte Complexation Study: The Effect of Polyion Charge Density and Chemical Nature of the CounterionsSeručnik, Mojca / Podlipnik, Črtomir / Hribar-Lee, Barbara et al. | 2018
- 5389
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Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon MutationBarlow, Kyle A. / Ó Conchúir, Shane / Thompson, Samuel / Suresh, Pooja / Lucas, James E. / Heinonen, Markus / Kortemme, Tanja et al. | 2018
- 5400
-
Theory for the Liquid–Liquid Phase Separation in Aqueous Antibody SolutionsKastelic, Miha / Vlachy, Vojko et al. | 2018
- 5409
-
Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network ModelsSankar, Kannan / Mishra, Sambit K. / Jernigan, Robert L. et al. | 2018
- 5418
-
A Lattice Model of Charge-Pattern-Dependent Polyampholyte Phase SeparationDas, Suman / Eisen, Adam / Lin, Yi-Hsuan / Chan, Hue Sun et al. | 2018
- 5432
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Water Adsorption on Clean and Defective Anatase TiO2 (001) Nanotube Surfaces: A Surface Science ApproachKenmoe, Stephane / Lisovski, Oleg / Piskunov, Sergei / Bocharov, Dmitry / Zhukovskii, Yuri F. / Spohr, Eckhard et al. | 2018
- 5441
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Lattice Models of Bacterial NucleoidsGoodsell, David S. / Autin, Ludovic / Olson, Arthur J. et al. | 2018
- 5448
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Online Optimization of Total Acceptance in Hamiltonian Replica Exchange SimulationsMacCallum, Justin L. / Muniyat, Mir Ishruna / Gaalswyk, Kari et al. | 2018
- 5458
-
Phase Equilibria of Polydisperse Square-Well Chain Fluid Confined in Random Porous Media: TPT of Wertheim and Scaled Particle TheoryHvozd, Taras V. / Kalyuzhnyi, Yurij V. / Cummings, Peter T. et al. | 2018
- 5466
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Biomolecular Simulations under Realistic Macroscopic Salt ConditionsRoss, Gregory A. / Rustenburg, Ariën S. / Grinaway, Patrick B. / Fass, Josh / Chodera, John D. et al. | 2018
- 5487
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Exploring the Underlying Mechanisms of the Xenopus laevis Embryonic Cell CycleZhang, Kun / Wang, Jin et al. | 2018
- 5500
-
Replica Ornstein–Zernike Theory Applied for Studying the Equilibrium Distribution of Electrolytes across Model MembranesHribar-Lee, Barbara / Lukšič, Miha et al. | 2018
- 5508
-
Metadynamics Enhanced Markov Modeling of Protein DynamicsBiswas, Mithun / Lickert, Benjamin / Stock, Gerhard et al. | 2018
- 5515
-
Convergence of Kirkwood–Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics SimulationsMilzetti, Jasmin / Nayar, Divya / van der Vegt, Nico F. A. et al. | 2018
- 5527
-
Quasiharmonic Analysis of the Energy Landscapes of Dihydrofolate Reductase from Piezophiles and MesophilesHuang, Qi / Rodgers, Jocelyn M. / Hemley, Russell J. / Ichiye, Toshiko et al. | 2018
- 5534
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Isotropic–Nematic Transition and Demixing Behavior in Binary Mixtures of Hard Spheres and Hard Spherocylinders Confined in a Disordered Porous Medium: Scaled Particle TheoryHvozd, M. / Patsahan, T. / Holovko, M. et al. | 2018
- 5547
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Inverse Design of Self-Assembling Frank-Kasper Phases and Insights Into Emergent QuasicrystalsLindquist, Beth A. / Jadrich, Ryan B. / Piñeros, William D. / Truskett, Thomas M. et al. | 2018
- 5557
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Effects of Trimethylamine‑N‑oxide (TMAO) on Hydrophobic and Charged InteractionsSu, Zhaoqian / Ravindhran, Gopal / Dias, Cristiano L. et al. | 2018
- 5567
-
Theory of Sequence Effects in Amyloid AggregationHuang, Caleb / Ghanati, Elaheh / Schmit, Jeremy D. et al. | 2018
- 5579
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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte CarloGill, Samuel C. / Lim, Nathan M. / Grinaway, Patrick B. / Rustenburg, Ariën S. / Fass, Josh / Ross, Gregory A. / Chodera, John D. / Mobley, David L. et al. | 2018
- 5599
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Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular DiffusionFennell, Christopher J. / Ghousifam, Neda / Haseleu, Jennifer M. / Gappa-Fahlenkamp, Heather et al. | 2018
- 5610
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Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and ParameterizationGe, Yunhui / Voelz, Vincent A. et al. | 2018
- 5623
-
Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1Campitelli, Paul / Guo, Jingjing / Zhou, Huan-Xiang / Ozkan, S. Banu et al. | 2018
- 5630
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Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics SimulationsLinke, Max / Köfinger, Jürgen / Hummer, Gerhard et al. | 2018
- 5640
-
Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular SimulationsDuboué-Dijon, Elise / Delcroix, Pauline / Martinez-Seara, Hector / Hladílková, Jana / Coufal, Pavel / Křížek, Tomáš / Jungwirth, Pavel et al. | 2018
- 5649
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Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic SimulationsPaul, Fabian / Noé, Frank / Weikl, Thomas R. et al. | 2018
- 5657
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Structural Modulation of Human Amylin Protofilaments by Naturally Occurring MutationsTofoleanu, Florentina / Yuan, Ye / Pickard, Frank C. / Tywoniuk, Bartłomiej / Brooks, Bernard R. / Buchete, Nicolae-Viorel et al. | 2018
- 5666
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Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden SpeciesFirman, Taylor / Wedekind, Stephen / McMorrow, T. J. / Ghosh, Kingshuk et al. | 2018
- 5678
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Transferable Coarse-Grained Models of Liquid–Liquid Equilibrium Using Local Density Potentials Optimized with the Relative EntropySanyal, Tanmoy / Shell, M. Scott et al. | 2018
- 5694
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Insights into the Structure of Liquid Water from Nuclear Quantum Effects on the Density and Compressibility of Ice PolymorphsPamuk, Betül / Allen, P. B. / Fernández-Serra, M.-V. et al. | 2018
- 5707
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A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-CageUralcan, Betul / Kim, Sang Beom / Markwalter, Chester E. / Prud’homme, Robert K. / Debenedetti, Pablo G. et al. | 2018
- 5716
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Predicting the Binding Mode of 2‑Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH TheoryHayashino, Yuji / Sugita, Masatake / Arima, Hidetoshi / Irie, Tetsumi / Kikuchi, Takeshi / Hirata, Fumio et al. | 2018