Bibliography
Here is the complete list of the published papers connected to the projects deposited in PLUMED-NEST:
[plumID:24.000] F. Mambretti, U. Raucci, M. Yang, M. Parrinello, How Does Structural Disorder Impact Heterogeneous Catalysts? The Case of Ammonia Decomposition on Non-stoichiometric Lithium Imide. ACS Catalysis. 14, 1252–1256 (2024)
[plumID:23.036] R. Wang, S. Mehdi, Z. Zou, P. Tiwary, Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution? The Journal of Physical Chemistry B. 128, 1012–1021 (2024)
[plumID:23.026] F. M. Dietrich, X. R. Advincula, G. Gobbo, M. A. Bellucci, M. Salvalaglio, Machine Learning Nucleation Collective Variables with Graph Neural Networks. Journal of Chemical Theory and Computation. 20, 1600–1611 (2023)
[plumID:23.016] J. C. Calderón, P. Ibrahim, D. Gobbo, F. L. Gervasio, T. Clark, Activation/Deactivation Free-Energy Profiles for the β2-Adrenergic Receptor: Ligand Modes of Action. Journal of Chemical Information and Modeling. 63, 6332–6343 (2023)
[plumID:23.006] M. Lüking, D. van der Spoel, J. Elf, G. A. Tribello, Can molecular dynamics be used to simulate biomolecular recognition? The Journal of Chemical Physics. 158 (2023)
[plumID:22.042] H. Wang, S. R. A. Rizvi, D. Dong, J. Lou, Q. Wang, W. Sopipong, Y. Su, F. Najar, P. K. Agarwal, F. Kozielski, S. Haider, Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16 (2023)
[plumID:22.032] I. Kolossváry, W. Sherman, Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint. The Journal of Physical Chemistry B. 127, 5214–5229 (2023)
[plumID:22.022] C. Arend, I. L. Grothaus, M. Waespy, L. C. Ciacchi, R. Dringen, Modulation of Multidrug Resistance Protein 1-mediated Transport Processes by the Antiviral Drug Ritonavir in Cultured Primary Astrocytes. Neurochemical Research. 49, 66–84 (2023)
[plumID:22.012] S. M. Ayala Mariscal, M. L. Pigazzini, Y. Richter, M. Özel, I. L. Grothaus, J. Protze, K. Ziege, M. Kulke, M. ElBediwi, J. V. Vermaas, L. Colombi Ciacchi, S. Köppen, F. Liu, J. Kirstein, Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT. Nature Communications. 13 (2022)
[plumID:22.001] B. Pampel, O. Valsson, Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials. Journal of Chemical Theory and Computation. 18, 4127–4141 (2022)
[plumID:21.044] A. R. Finney, M. Salvalaglio, Multiple pathways in NaCl homogeneous crystal nucleation. Faraday Discussions. 235, 56–80 (2022)
[plumID:21.034] D. Wang, Y. Wang, J. Chang, L. Zhang, H. Wang, W. E., Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics. Nature Computational Science. 2, 20–29 (2021)
[plumID:21.024] D. Trapl, M. Krupička, V. Višňovský, J. Hozzová, J. Ol’ha, A. Křenek, V. Spiwok, Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. 62, 567–576 (2022)
[plumID:21.014] C. Paissoni, C. Camilloni, How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case. Frontiers in Molecular Biosciences. 8 (2021)
[plumID:21.004] M. Bertazzo, D. Gobbo, S. Decherchi, A. Cavalli, Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy. Journal of Chemical Theory and Computation. 17, 5287–5300 (2021)
[plumID:20.029] D. Saad, C. Paissoni, A. Chaves-Sanjuan, M. Nardini, R. Mantovani, N. Gnesutta, C. Camilloni, High Conformational Flexibility of the E2F1/DP1/DNA Complex. Journal of Molecular Biology. 433, 167119 (2021)
[plumID:20.019] N. F. Francia, L. S. Price, J. Nyman, S. L. Price, M. Salvalaglio, Systematic Finite-Temperature Reduction of Crystal Energy Landscapes. Crystal Growth & Design. 20, 6847–6862 (2020)
[plumID:20.009] A. Jussupow, A. C. Messias, R. Stehle, A. Geerlof, S. M. Ø. Solbak, C. Paissoni, A. Bach, M. Sattler, C. Camilloni, The dynamics of linear polyubiquitin. Science Advances. 6 (2020)
[plumID:19.083] V. Rizzi, D. Mendels, E. Sicilia, M. Parrinello, Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis. Journal of Chemical Theory and Computation. 15, 4507–4515 (2019)
[plumID:19.073] L. Kollias, D. C. Cantu, V. Glezakou, R. Rousseau, M. Salvalaglio, On the Role of Enthalpic and Entropic Contributions to the Conformational Free Energy Landscape of MIL‐101(Cr) Secondary Building Units. Advanced Theory and Simulations. 3 (2020)
[plumID:19.063] M. Bernetti, M. Masetti, M. Recanatini, R. E. Amaro, A. Cavalli, An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes. Journal of Chemical Theory and Computation. 15, 5689–5702 (2019)
[plumID:19.053] E. Baldi, M. Ceriotti, G. A. Tribello, Extracting the interfacial free energy and anisotropy from a smooth fluctuating dividing surface. Journal of Physics: Condensed Matter. 29, 445001 (2017)
[plumID:19.043] G. Piccini, D. Mendels, M. Parrinello, Metadynamics with Discriminants: A Tool for Understanding Chemistry. Journal of Chemical Theory and Computation. 14, 5040–5044 (2018)
[plumID:19.023] A. Gil-Ley, G. Bussi, Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering. Journal of Chemical Theory and Computation. 11, 1077–1085 (2015)
[plumID:19.013] A. Cesari, S. Bottaro, K. Lindorff-Larsen, P. Banáš, J. Šponer, G. Bussi, Fitting Corrections to an RNA Force Field Using Experimental Data. Journal of Chemical Theory and Computation. 15, 3425–3431 (2019)
[plumID:19.003] S. Vahidi, Z. A. Ripstein, M. Bonomi, T. Yuwen, M. F. Mabanglo, J. B. Juravsky, K. Rizzolo, A. Velyvis, W. A. Houry, M. Vendruscolo, J. L. Rubinstein, L. E. Kay, Reversible inhibition of the ClpP protease via an N-terminal conformational switch. Proceedings of the National Academy of Sciences. 115 (2018)
[plumID:23.046] G. C. A. da Hora, M. Oh, J. D. M. Nguyen, J. M. J. Swanson, One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates. The Journal of Physical Chemistry B (2024)
[plumID:23.035] J. C. Calderón, E. Plut, M. Keller, C. Cabrele, O. Reiser, F. L. Gervasio, T. Clark, Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. Journal of Chemical Information and Modeling. 64, 205–218 (2023)
[plumID:23.025] M. D. Polêto, J. A. Lemkul, Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. Journal of Chemical Information and Modeling. 63, 6851–6862 (2023)
[plumID:23.015] V. Tiwari, T. Karmakar, Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters. The Journal of Physical Chemistry Letters. 14, 6686–6694 (2023)
[plumID:23.005] J. C. Calderón, P. Ibrahim, D. Gobbo, F. L. Gervasio, T. Clark, General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. Journal of Chemical Information and Modeling. 63, 3105–3117 (2023)
[plumID:22.041] M. Invernizzi, A. Krämer, C. Clementi, F. Noé, Skipping the Replica Exchange Ladder with Normalizing Flows. The Journal of Physical Chemistry Letters. 13, 11643–11649 (2022)
[plumID:22.031] D. Ray, N. Ansari, V. Rizzi, M. Invernizzi, M. Parrinello, Rare Event Kinetics from Adaptive Bias Enhanced Sampling. Journal of Chemical Theory and Computation. 18, 6500–6509 (2022)
[plumID:22.021] S. L. Bore, P. M. Piaggi, R. Car, F. Paesani, Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations. The Journal of Chemical Physics. 157 (2022)
[plumID:22.011] S. Mehdi, D. Wang, S. Pant, P. Tiwary, Accelerating All-Atom Simulations and Gaining Mechanistic Understanding of Biophysical Systems through State Predictive Information Bottleneck. Journal of Chemical Theory and Computation. 18, 3231–3238 (2022)
[plumID:22.000] X. Lu, J. Huang, A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase. Communications Biology. 5 (2022)
[plumID:21.043] H. Lu, J. Martí, Predicting the conformational variability of oncogenic GTP-bound G12D mutated KRas-4B proteins at zwitterionic model cell membranes. Nanoscale. 14, 3148–3158 (2022)
[plumID:21.033] A. Pérez de Alba Ortíz, J. Vreede, B. Ensing, Sequence dependence of transient Hoogsteen base pairing in DNA. PLOS Computational Biology. 18, e1010113 (2022)
[plumID:21.023] J. Rydzewski, O. Valsson, Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling. The Journal of Physical Chemistry A. 125, 6286–6302 (2021)
[plumID:21.013] K. M. Bal, E. C. Neyts, Quantifying the impact of vibrational nonequilibrium in plasma catalysis: insights from a molecular dynamics model of dissociative chemisorption. Journal of Physics D: Applied Physics. 54, 394004 (2021)
[plumID:21.003] M. C. Ahmed, L. K. Skaanning, A. Jussupow, E. A. Newcombe, B. B. Kragelund, C. Camilloni, A. E. Langkilde, K. Lindorff-Larsen, Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods. Frontiers in Molecular Biosciences. 8 (2021)
[plumID:20.028] H. Lu, J. Martí, Long-lasting Salt Bridges Provide the Anchoring Mechanism of Oncogenic Kirsten Rat Sarcoma Proteins at Cell Membranes. The Journal of Physical Chemistry Letters. 11, 9938–9945 (2020)
[plumID:20.018] K. M. Bal, S. Fukuhara, Y. Shibuta, E. C. Neyts, Free energy barriers from biased molecular dynamics simulations. The Journal of Chemical Physics. 153 (2020)
[plumID:20.008] K. Rossi, V. Jurásková, R. Wischert, L. Garel, C. Corminbœuf, M. Ceriotti, Simulating Solvation and Acidity in Complex Mixtures with First-Principles Accuracy: The Case of CH3SO3H and H2O2 in Phenol. Journal of Chemical Theory and Computation. 16, 5139–5149 (2020)
[plumID:19.082] V. Rizzi, D. Polino, E. Sicilia, N. Russo, M. Parrinello, The Onset of Dehydrogenation in Solid Ammonia Borane: An Ab Initio Metadynamics Study. Angewandte Chemie International Edition. 58, 3976–3980 (2019)
[plumID:19.072] S. Reißer, S. Zucchelli, S. Gustincich, G. Bussi, Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data. Nucleic Acids Research. 48, 1164–1174 (2019)
[plumID:19.062] J. Smith, P. McMullen, Z. Yuan, J. Pfaendtner, S. Jiang, Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules. 21, 435–443 (2019)
[plumID:19.052] B. Cheng, G. A. Tribello, M. Ceriotti, The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147 (2017)
[plumID:19.042] D. Mendels, G. Piccini, M. Parrinello, Collective Variables from Local Fluctuations. The Journal of Physical Chemistry Letters. 9, 2776–2781 (2018)
[plumID:19.032] F. Pietrucci, A. M. Saitta, Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios. Proceedings of the National Academy of Sciences. 112, 15030–15035 (2015)
[plumID:19.022] H. Chen, H. Fu, X. Shao, C. Chipot, W. Cai, ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. Journal of Chemical Information and Modeling. 58, 1315–1318 (2018)
[plumID:19.012] C. Paissoni, A. Jussupow, C. Camilloni, Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data. Journal of Applied Crystallography. 52, 394–402 (2019)
[plumID:19.002] M. Bonomi, R. Pellarin, M. Vendruscolo, Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy. Biophysical Journal. 114, 1604–1613 (2018)
[plumID:24.008] K. A. Croney, J. McCarty, Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. The Journal of Physical Chemistry B. 128, 3102–3112 (2024)
[plumID:23.045] V. M. D’Amore, P. Conflitti, L. Marinelli, V. Limongelli, Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state (2023)
[plumID:23.034] R. Zhao, Z. Zou, J. D. Weeks, P. Tiwary, Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water. Journal of Chemical Theory and Computation. 19, 9093–9101 (2023)
[plumID:23.024] N. S. M. Herringer, S. Dasetty, D. Gandhi, J. Lee, A. L. Ferguson, Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables. Journal of Chemical Theory and Computation. 20, 178–198 (2023)
[plumID:23.014] D. Di Marino, P. Conflitti, S. Motta, V. Limongelli, Structural basis of dimerization of chemokine receptors CCR5 and CXCR4. Nature Communications. 14 (2023)
[plumID:23.004] P. M. Piaggi, T. E. Gartner, R. Car, P. G. Debenedetti, Melting curves of ice polymorphs in the vicinity of the liquid–liquid critical point. The Journal of Chemical Physics. 159 (2023)
[plumID:22.040] M. Wieczór, P. K. Tang, M. Orozco, P. Cossio, From Closed to Open: Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure. SSRN Electronic Journal (2022)
[plumID:22.030] Y. Wang, L. Herron, P. Tiwary, From data to noise to data for mixing physics across temperatures with generative artificial intelligence. Proceedings of the National Academy of Sciences. 119 (2022)
[plumID:22.020] W. He, N. Naleem, D. Kleiman, S. Kirmizialtin, Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA. The Journal of Physical Chemistry Letters. 13, 3400–3408 (2022)
[plumID:22.009] T.-R. Li, F. Huck, G. Piccini, K. Tiefenbacher, Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations. Nature Chemistry. 14, 985–994 (2022)
[plumID:21.052] V. Marinova, G. P. F. Wood, I. Marziano, M. Salvalaglio, Investigating the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets. Crystal Growth & Design. 22, 3034–3041 (2022)
[plumID:21.042] B. Jin, F. Yan, X. Qi, B. Cai, J. Tao, X. Fu, S. Tan, P. Zhang, J. Pfaendtner, N. Y. Naser, F. Baneyx, X. Zhang, J. J. DeYoreo, C. Chen, Peptoid‐Directed Formation of Five‐Fold Twinned Au Nanostars through Particle Attachment and Facet Stabilization. Angewandte Chemie. 134 (2022)
[plumID:21.032] M. D. Peris-Díaz, R. Guran, C. Domene, V. de los Rios, O. Zitka, V. Adam, A. Krężel, An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species. Journal of the American Chemical Society. 143, 16486–16501 (2021)
[plumID:21.022] X. Qi, Y. Zhao, K. Lachowski, J. Boese, Y. Cai, O. Dollar, B. Hellner, L. Pozzo, J. Pfaendtner, J. Chun, F. Baneyx, C. J. Mundy, Predictive Theoretical Framework for Dynamic Control of Bioinspired Hybrid Nanoparticle Self-Assembly. ACS Nano. 16, 1919–1928 (2022)
[plumID:21.012] S. R. Summers, S. Alamdari, C. J. Kraft, R. Brunecky, J. Pfaendtner, J. L. Kaar, Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus. Protein Engineering, Design and Selection. 34 (2021)
[plumID:21.002] P. M. Piaggi, A. Z. Panagiotopoulos, P. G. Debenedetti, R. Car, Phase Equilibrium of Water with Hexagonal and Cubic Ice Using the SCAN Functional. Journal of Chemical Theory and Computation. 17, 3065–3077 (2021)
[plumID:20.027] K. Abdel-Maksoud, M. A. al-Badri, C. Lorenz, J. W. Essex, Allosteric Regulation of SARS-CoV-2 Protease: Towards Informed Structure-Based Drug Discovery (2020)
[plumID:20.017] M. J. Hartmann, Y. Singh, E. Vanden-Eijnden, G. M. Hocky, Infinite switch simulated tempering in force (FISST). The Journal of Chemical Physics. 152 (2020)
[plumID:20.007] Z. Smith, P. Ravindra, Y. Wang, R. Cooley, P. Tiwary, Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics. The Journal of Physical Chemistry B. 124, 8221–8229 (2020)
[plumID:19.081] P. M. Piaggi, M. Parrinello, Calculation of phase diagrams in the multithermal-multibaric ensemble. The Journal of Chemical Physics. 150 (2019)
[plumID:19.071] V. Marinova, M. Salvalaglio, Time-independent free energies from metadynamics via mean force integration. The Journal of Chemical Physics. 151 (2019)
[plumID:19.061] E. Jackson, M. Miklitz, Q. Song, G. A. Tribello, K. E. Jelfs, Computational Evaluation of the Diffusion Mechanisms for C8 Aromatics in Porous Organic Cages. The Journal of Physical Chemistry C. 123, 21011–21021 (2019)
[plumID:19.051] B. Cheng, G. A. Tribello, M. Ceriotti, Solid-liquid interfacial free energy out of equilibrium. Physical Review B. 92 (2015)
[plumID:19.041] C. M. Mao, J. Sampath, K. G. Sprenger, G. Drobny, J. Pfaendtner, Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. Langmuir. 35, 5911–5920 (2019)
[plumID:19.031] S. Pipolo, M. Salanne, G. Ferlat, S. Klotz, A. M. Saitta, F. Pietrucci, Navigating at Will on the Water Phase Diagram. Physical Review Letters. 119 (2017)
[plumID:19.021] G. M. Hocky, T. Dannenhoffer-Lafage, G. A. Voth, Coarse-Grained Directed Simulation. Journal of Chemical Theory and Computation. 13, 4593–4603 (2017)
[plumID:19.011] T. Giorgino, How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation. Computer Physics Communications. 228, 258–263 (2018)
[plumID:19.001] V. Mlýnský, G. Bussi, Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility. The Journal of Physical Chemistry Letters. 9, 313–318 (2018)
[plumID:24.007] A. Borsatto, E. Gianquinto, V. Rizzi, F. L. Gervasio, SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein–Protein Interfaces. Journal of Chemical Theory and Computation (2024)
[plumID:23.044] F. M. Steudel, E. Ubasart, L. Leanza, M. Pujals, T. Parella, G. M. Pavan, X. Ribas, M. von Delius, Synthesis of C60/[10]CPP‐Catenanes by Regioselective, Nanocapsule‐Templated Bingel Bis‐Addition. Angewandte Chemie International Edition. 62 (2023)
[plumID:23.033] P. Pokorná, V. Mlýnský, G. Bussi, J. Šponer, P. Stadlbauer, Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble. International Journal of Biological Macromolecules. 261, 129712 (2024)
[plumID:23.023] K. Torkelson, N. Y. Naser, X. Qi, Z. Li, W. Yang, K. Pushpavanam, C.-L. Chen, F. Baneyx, J. Pfaendtner, Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications. Chemistry of Materials. 36, 786–794 (2024)
[plumID:23.013] I. Kolossváry, W. Sherman, Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint. The Journal of Physical Chemistry B. 127, 5214–5229 (2023)
[plumID:23.003] W.-T. Hsu, V. Piomponi, P. T. Merz, G. Bussi, M. R. Shirts, Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of Chemical Theory and Computation. 19, 1805–1817 (2023)
[plumID:22.039] Z. Zou, E. R. Beyerle, S.-T. Tsai, P. Tiwary, Driving and characterizing nucleation of urea and glycine polymorphs in water. Proceedings of the National Academy of Sciences. 120 (2023)
[plumID:22.029] L. A. Chi, S. Asgharpour, J. Correa-Basurto, C. R. Bandala, M. Martínez-Archundia, Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations. Journal of Computer-Aided Molecular Design. 36, 653–675 (2022)
[plumID:22.019] R. Bobrovs, E. E. Basens, L. Drunka, I. Kanepe, S. Matisone, K. K. Velins, V. Andrianov, G. Leitis, D. Zelencova-Gopejenko, D. Rasina, A. Jirgensons, K. Jaudzems, Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials. Journal of Chemical Information and Modeling. 62, 3263–3273 (2022)
[plumID:22.008] D. Sucerquia, C. Parra, P. Cossio, O. Lopez-Acevedo, Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters. The Journal of Chemical Physics. 156 (2022)
[plumID:21.051] T. Fröhlking, V. Mlýnský, M. Janeček, P. Kührová, M. Krepl, P. Banáš, J. Šponer, G. Bussi, Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of Chemical Theory and Computation. 18, 4490–4502 (2022)
[plumID:21.041] M. Badin, R. Martoňák, Nucleating a Different Coordination in a Crystal under Pressure: A Study of the
[plumID:21.031] K. Walczewska-Szewc, W. Nowak, Photo-Switchable Sulfonylureas Binding to ATP-Sensitive Potassium Channel Reveal the Mechanism of Light-Controlled Insulin Release. The Journal of Physical Chemistry B. 125, 13111–13121 (2021)
[plumID:21.021] F. Giberti, G. A. Tribello, M. Ceriotti, Global Free-Energy Landscapes as a Smoothly Joined Collection of Local Maps. Journal of Chemical Theory and Computation. 17, 3292–3308 (2021)
[plumID:21.011] A. R. Finney, I. J. McPherson, P. R. Unwin, M. Salvalaglio, Electrochemistry, ion adsorption and dynamics in the double layer: a study of NaCl(aq) on graphite. Chemical Science. 12, 11166–11180 (2021)
[plumID:21.001] T. F. Gesteira, T. D. Marforio, J. W. Mueller, M. Calvaresi, V. J. Coulson-Thomas, Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases. ACS Catalysis. 11, 10974–10987 (2021)
[plumID:20.026] B. L. Peters, J. Deng, A. L. Ferguson, Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor. PLOS ONE. 15, e0243313 (2020)
[plumID:20.016] P. M. Piaggi, M. Parrinello, Predicting polymorphism in molecular crystals using orientational entropy. Proceedings of the National Academy of Sciences. 115, 10251–10256 (2018)
[plumID:20.006] G. Mattedi, S. Acosta-Gutiérrez, T. Clark, F. L. Gervasio, A combined activation mechanism for the glucagon receptor. Proceedings of the National Academy of Sciences. 117, 15414–15422 (2020)
[plumID:19.080] K. M. Bal, A. Bogaerts, E. C. Neyts, Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium. The Journal of Physical Chemistry Letters. 11, 401–406 (2019)
[plumID:19.070] S. Bottaro, P. J. Nichols, B. Vögeli, M. Parrinello, K. Lindorff-Larsen, Integrating NMR and simulations reveals motions in the UUCG tetraloop. Nucleic Acids Research. 48, 5839–5848 (2020)
[plumID:19.060] L. Bonati, Y.-Y. Zhang, M. Parrinello, Neural networks-based variationally enhanced sampling. Proceedings of the National Academy of Sciences. 116, 17641–17647 (2019)
[plumID:19.050] J. Klug, C. Triguero, M. G. Del Pópolo, G. A. Tribello, Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes. The Journal of Physical Chemistry B. 122, 6417–6422 (2018)
[plumID:19.040] L. Hovan, F. Comitani, F. L. Gervasio, Defining an Optimal Metric for the Path Collective Variables. Journal of Chemical Theory and Computation. 15, 25–32 (2018)
[plumID:19.030] M. Lelimousin, V. Limongelli, M. S. P. Sansom, Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations. Journal of the American Chemical Society. 138, 10611–10622 (2016)
[plumID:19.020] M. Bernetti, M. Masetti, F. Pietrucci, M. Blackledge, M. R. Jensen, M. Recanatini, L. Mollica, A. Cavalli, Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations. The Journal of Physical Chemistry B. 121, 9572–9582 (2017)
[plumID:19.010] B. Weber, M. Hora, P. Kazman, C. Göbl, C. Camilloni, B. Reif, J. Buchner, The Antibody Light-Chain Linker Regulates Domain Orientation and Amyloidogenicity. Journal of Molecular Biology. 430, 4925–4940 (2018)
[plumID:19.000] M. Invernizzi, M. Parrinello, Making the Best of a Bad Situation: A Multiscale Approach to Free Energy Calculation. Journal of Chemical Theory and Computation. 15, 2187–2194 (2019)
[plumID:24.006] S. Zhong, Z. Shi, B. Zhang, Z. Wen, L. Chen, Homogeneous water vapor condensation with a deep neural network potential model. The Journal of Chemical Physics. 160 (2024)
[plumID:23.043] L. Gigli, A. Goscinski, M. Ceriotti, G. A. Tribello. Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling
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[plumID:22.028] I. L. Grothaus, G. Bussi, L. Colombi Ciacchi, Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. Journal of Chemical Information and Modeling. 62, 4992–5008 (2022)
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[plumID:23.029] F. Ballabio, C. Paissoni, M. Bollati, M. de Rosa, R. Capelli, C. Camilloni, Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations. Journal of Chemical Theory and Computation. 19, 8401–8413 (2023)
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[plumID:23.018] K. J. Lachowski, H. T. Chiang, K. Torkelson, W. Zhou, S. Zhang, J. Pfaendtner, L. D. Pozzo, Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention. Langmuir. 39, 15878–15888 (2023)
[plumID:23.008] F. Pesce, K. Lindorff-Larsen, Combining Experiments and Simulations to Examine the Temperature-Dependent Behavior of a Disordered Protein. The Journal of Physical Chemistry B. 127, 6277–6286 (2023)
[plumID:22.044] A. R. Finney, M. Salvalaglio, A variational approach to assess reaction coordinates for two-step crystallization. The Journal of Chemical Physics. 158 (2023)
[plumID:22.034] I. J. Sugden, N. F. Francia, T. Jensen, C. S. Adjiman, M. Salvalaglio, Rationalising the difference in crystallisability of two sulflowers using efficient in silico methods. CrystEngComm. 24, 6830–6838 (2022)
[plumID:22.024] T. Löhr, P. Sormanni, M. Vendruscolo, Conformational Entropy as a Potential Liability of Computationally Designed Antibodies. Biomolecules. 12, 718 (2022)
[plumID:22.014] J. Shi, M. Fulford, H. Li, M. Marzook, M. Reisjalali, M. Salvalaglio, C. Molteni, Investigating the quasi-liquid layer on ice surfaces: a comparison of order parameters. Physical Chemistry Chemical Physics. 24, 12476–12487 (2022)
[plumID:22.003] M. Invernizzi, M. Parrinello, Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling. Journal of Chemical Theory and Computation. 18, 3988–3996 (2022)
[plumID:21.046] M. Lambrughi, E. Maiani, B. Aykac Fas, G. S. Shaw, B. B. Kragelund, K. Lindorff-Larsen, K. Teilum, G. Invernizzi, E. Papaleo, Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs. Frontiers in Molecular Biosciences. 8 (2021)
[plumID:21.036] L. Li, T. Casalini, P. Arosio, M. Salvalaglio, Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations. Journal of Chemical Theory and Computation. 18, 1915–1928 (2022)
[plumID:21.026] F. Colizzi, M. Orozco, Probing allosteric regulations with coevolution-driven molecular simulations. Science Advances. 7 (2021)
[plumID:21.016] M. Bernetti, K. B. Hall, G. Bussi, Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles. Nucleic Acids Research. 49, e84–e84 (2021)
[plumID:21.006] M. Invernizzi, OPES: On-the-fly Probability Enhanced Sampling method, Il Nuovo Cimento C 4, 112 (2021)
[plumID:20.031] C. Cozza, F. M. Raymo, A. Pietropaolo, Shape factors in the binding of soft fluorescent nanoshuttles with target receptors. Molecular Systems Design & Engineering. 6, 281–285 (2021)
[plumID:20.021] E. Karlsson, C. Paissoni, A. M. Erkelens, Z. A. Tehranizadeh, F. A. Sorgenfrei, E. Andersson, W. Ye, C. Camilloni, P. Jemth, Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. Journal of Biological Chemistry. 295, 17698–17712 (2020)
[plumID:20.011] J. Smith, J. Pfaendtner, Elucidating the Molecular Interactions between Uremic Toxins and the Sudlow II Binding Site of Human Serum Albumin. The Journal of Physical Chemistry B. 124, 3922–3930 (2020)
[plumID:20.001] B. M. Sala, T. Le Marchand, G. Pintacuda, C. Camilloni, A. Natalello, S. Ricagno, Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophysical Journal. 119, 978–988 (2020)
[plumID:19.075] T. Giorgino, PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python. Journal of Open Source Software. 4, 1773 (2019)
[plumID:19.065] W. Chen, A. L. Ferguson, Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration. Journal of Computational Chemistry. 39, 2079–2102 (2018)
[plumID:19.055] Z. Šućur, V. Spiwok, Sampling Enhancement and Free Energy Prediction by the Flying Gaussian Method. Journal of Chemical Theory and Computation. 12, 4644–4650 (2016)
[plumID:19.045] M. De La Pierre, P. Raiteri, A. G. Stack, J. D. Gale, Uncovering the Atomistic Mechanism for Calcite Step Growth. Angewandte Chemie International Edition. 56, 8464–8467 (2017)
[plumID:19.035] D. Meral, D. Provasi, D. Prada-Gracia, J. Möller, K. Marino, M. J. Lohse, M. Filizola, Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations. Scientific Reports. 8 (2018)
[plumID:19.025] T. Löhr, A. Jussupow, C. Camilloni, Metadynamic metainference: Convergence towards force field independent structural ensembles of a disordered peptide. The Journal of Chemical Physics. 146 (2017)
[plumID:19.015] V. Marinova, G. P. F. Wood, I. Marziano, M. Salvalaglio, Dynamics and Thermodynamics of Ibuprofen Conformational Isomerism at the Crystal/Solution Interface. Journal of Chemical Theory and Computation. 14, 6484–6494 (2018)
[plumID:19.005] G. T. Heller, F. A. Aprile, M. Bonomi, C. Camilloni, A. De Simone, M. Vendruscolo, Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide. Journal of Molecular Biology. 429, 2772–2779 (2017)
[plumID:24.001] D. Ray, S. Das, U. Raucci, Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. Journal of Chemical Information and Modeling (2024)
[plumID:23.037] X. Qi, J. Pfaendtner, High-Throughput Computational Screening of Solid-Binding Peptides. Journal of Chemical Theory and Computation. 20, 2959–2968 (2024)
[plumID:23.027] A. R. Finney, M. Salvalaglio, Properties of aqueous electrolyte solutions at carbon electrodes: effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer. Faraday Discussions. 249, 334–362 (2024)
[plumID:23.017] S. Das, U. Raucci, R. P. P. Neves, M. J. Ramos, M. Parrinello, How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques. ACS Catalysis. 13, 8092–8098 (2023)
[plumID:23.007] S. Alamdari, J. Pfaendtner, Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains. The Journal of Physical Chemistry B. 127, 6163–6170 (2023)
[plumID:22.043] K. Rahimi, P. M. Piaggi, G. H. Zerze, Comparison of On-the-Fly Probability Enhanced Sampling and Parallel Tempering Combined with Metadynamics for Atomistic Simulations of RNA Tetraloop Folding. The Journal of Physical Chemistry B. 127, 4722–4732 (2023)
[plumID:22.033] I. Kolossváry, W. Sherman, Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint. The Journal of Physical Chemistry B. 127, 5214–5229 (2023)
[plumID:22.023] Z. Faidon Brotzakis, T. Löhr, S. Truong, S. Hoff, M. Bonomi, M. Vendruscolo, Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy. Biochemistry. 62, 2407–2416 (2023)
[plumID:22.013] Y. Wang, S. Parmar, J. S. Schneekloth, P. Tiwary, Interrogating RNA–Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations. ACS Central Science. 8, 741–748 (2022)
[plumID:22.002] J. Debnath, M. Parrinello, Computing Rates and Understanding Unbinding Mechanisms in Host–Guest Systems. Journal of Chemical Theory and Computation. 18, 1314–1319 (2022)
[plumID:21.045] D. Maag, M. Putzu, C. L. Gómez-Flores, F. Gräter, M. Elstner, T. Kubař, Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein. Physical Chemistry Chemical Physics. 23, 26366–26375 (2021)
[plumID:21.035] A. R. Finney, M. Salvalaglio, Bridging the gap between mesoscopic and molecular models of solid/liquid interfaces out-of-equilibrium. Chemical Engineering Research and Design. 180, 285–295 (2022)
[plumID:21.025] Y. Karami, A. López-Castilla, A. Ori, J.-L. Thomassin, B. Bardiaux, T. Malliavin, N. Izadi-Pruneyre, O. Francetic, M. Nilges, Computational and biochemical analysis of type IV pilus dynamics and stability. Structure. 29, 1397-1409.e6 (2021)
[plumID:21.015] E. Madland, Z. Forsberg, Y. Wang, K. Lindorff-Larsen, A. Niebisch, J. Modregger, V. G. H. Eijsink, F. L. Aachmann, G. Courtade, Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. Journal of Biological Chemistry. 297, 101084 (2021)
[plumID:21.005] T. Karmakar, M. Invernizzi, V. Rizzi, M. Parrinello, Collective variables for the study of crystallisation. Molecular Physics. 119 (2021)
[plumID:20.030] C. Paissoni, S. Puri, I. Wang, S.-Y. Chen, C. Camilloni, S.-T. D. Hsu, Converging experimental and computational views of the knotting mechanism of a small knotted protein. Biophysical Journal. 120, 2276–2286 (2021)
[plumID:20.020] J. Pfaendtner, M. Bonomi, Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics. Journal of Chemical Theory and Computation. 11, 5062–5067 (2015)
[plumID:20.010] P. M. Piaggi, R. Car, Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations. The Journal of Chemical Physics. 152 (2020)
[plumID:20.000] R. Capelli, A. Bochicchio, G. Piccini, R. Casasnovas, P. Carloni, M. Parrinello, Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations. Journal of Chemical Theory and Computation. 15, 3354–3361 (2019)
[plumID:19.074] F. Colizzi, C. Perez-Gonzalez, R. Fritzen, Y. Levy, M. F. White, J. C. Penedo, G. Bussi, Asymmetric base-pair opening drives helicase unwinding dynamics. Proceedings of the National Academy of Sciences. 116, 22471–22477 (2019)
[plumID:19.064] J. Sampath, J. Pfaendtner, Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Molecular Physics. 117, 3642–3650 (2019)
[plumID:19.054] G. Piccini, M. Parrinello, Accurate Quantum Chemical Free Energies at Affordable Cost. The Journal of Physical Chemistry Letters. 10, 3727–3731 (2019)
[plumID:19.044] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle. Physical Review Letters. 122 (2019)
[plumID:19.024] M. Deighan, M. Bonomi, J. Pfaendtner, Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble. Journal of Chemical Theory and Computation. 8, 2189–2192 (2012)
[plumID:19.014] L. Kollias, D. C. Cantu, M. A. Tubbs, R. Rousseau, V.-A. Glezakou, M. Salvalaglio, Molecular Level Understanding of the Free Energy Landscape in Early Stages of Metal–Organic Framework Nucleation. Journal of the American Chemical Society. 141, 6073–6081 (2019)
[plumID:19.004] M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo, Metainference: A Bayesian inference method for heterogeneous systems. Science Advances. 2 (2016)