Bibliography

Here is the complete list of the published papers connected to the projects deposited in PLUMED-NEST:

[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 B1B2 Transition in NaCl by Metadynamics. Physical Review Letters. 127 (2021)

[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: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

[plumID:23.032] H. Hradiská, M. Kurečka, J. Beránek, G. Tedeschi, V. Višňovský, A. Křenek, V. Spiwok, Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics. The Journal of Physical Chemistry B. 128, 903–913 (2024)

[plumID:23.022] L. Bonati, E. Trizio, A. Rizzi, M. Parrinello, A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar. The Journal of Chemical Physics. 159 (2023)

[plumID:23.012] 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:23.002] J. Lam, F. Pietrucci, Critical comparison of general-purpose collective variables for crystal nucleation. Physical Review E. 107 (2023)

[plumID:22.038] U. Raucci, D. M. Sanchez, T. J. Martínez, M. Parrinello, Enhanced Sampling Aided Design of Molecular Photoswitches. Journal of the American Chemical Society. 144, 19265–19271 (2022)

[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)

[plumID:22.018] K. Hutchinson, D. B. Silva, J. Bohlke, C. Clausen, A. A. Thomas, M. Bonomi, A. Schlessinger, Describing inhibitor specificity for the amino acid transporter LAT1 from metainference simulations. Biophysical Journal. 121, 4476–4491 (2022)

[plumID:22.007] A. Di Rita, D. F. Angelini, T. Maiorino, V. Caputo, R. Cascella, M. Kumar, M. Tiberti, M. Lambrughi, N. Wesch, F. Löhr, V. Dötsch, M. Carinci, P. D’Acunzo, V. Chiurchiù, E. Papaleo, V. V. Rogov, E. Giardina, L. Battistini, F. Strappazzon, Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy. Cell Death & Differentiation. 28, 2499–2516 (2021)

[plumID:21.050] J. Rosenau, I. L. Grothaus, Y. Yang, N. D. Kumar, L. C. Ciacchi, S. Kelm, M. Waespy, N-glycosylation modulates enzymatic activity of Trypanosoma congolense trans-sialidase. Journal of Biological Chemistry. 298, 102403 (2022)

[plumID:21.040] Z. F. Brotzakis, P. R. Lindstedt, R. J. Taylor, D. J. Rinauro, N. C. T. Gallagher, G. J. L. Bernardes, M. Vendruscolo, A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms. ACS Central Science. 7, 1986–1995 (2021)

[plumID:21.030] S. Alamdari, K. Torkelson, X. Wang, C.-L. Chen, A. L. Ferguson, J. Pfaendtner, Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains. The Journal of Physical Chemistry B. 127, 6171–6183 (2023)

[plumID:21.020] K. M. Bal, Reweighted Jarzynski Sampling: Acceleration of Rare Events and Free Energy Calculation with a Bias Potential Learned from Nonequilibrium Work. Journal of Chemical Theory and Computation. 17, 6766–6774 (2021)

[plumID:21.010] T. Magrino, F. Pietrucci, A. M. Saitta, Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry. The Journal of Physical Chemistry Letters. 12, 2630–2637 (2021)

[plumID:21.000] J. Ludwig, J. Smith, J. Pfaendtner, Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The Journal of Physical Chemistry B. 125, 2910–2920 (2021)

[plumID:20.025] V. Rizzi, L. Bonati, N. Ansari, M. Parrinello, The role of water in host-guest interaction. Nature Communications. 12 (2021)

[plumID:20.015] R.-A. A. Garibsingh, E. Ndaru, A. A. Garaeva, Y. Shi, L. Zielewicz, P. Zakrepine, M. Bonomi, D. J. Slotboom, C. Paulino, C. Grewer, A. Schlessinger, Rational design of ASCT2 inhibitors using an integrated experimental-computational approach. Proceedings of the National Academy of Sciences. 118 (2021)

[plumID:20.005] R. Capelli, W. Lyu, V. Bolnykh, S. Meloni, J. M. H. Olsen, U. Rothlisberger, M. Parrinello, P. Carloni, Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. The Journal of Physical Chemistry Letters. 11, 6373–6381 (2020)

[plumID:19.079] S. Alamdari, J. Pfaendtner, Impact of glutamate carboxylation in the adsorption of the α-1 domain of osteocalcin to hydroxyapatite and titania. Molecular Systems Design & Engineering. 5, 620–631 (2020)

[plumID:19.069] V. Marinova, G. P. F. Wood, I. Marziano, M. Salvalaglio, Solvent Dynamics and Thermodynamics at the Crystal–Solution Interface of Ibuprofen. Crystal Growth & Design. 19, 6534–6541 (2019)

[plumID:19.049] G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)

[plumID:19.039] V. Limongelli, M. Bonomi, M. Parrinello, Funnel metadynamics as accurate binding free-energy method. Proceedings of the National Academy of Sciences. 110, 6358–6363 (2013)

[plumID:19.029] P. Marinelli, S. Navarro, R. Graña-Montes, M. Bañó-Polo, M. R. Fernández, E. Papaleo, S. Ventura, A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation. Redox Biology. 14, 566–575 (2018)

[plumID:19.019] Y. Wang, O. Valsson, P. Tiwary, M. Parrinello, K. Lindorff-Larsen, Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149 (2018)

[plumID:19.009] S. Bottaro, P. Banáš, J. Šponer, G. Bussi, Free Energy Landscape of GAGA and UUCG RNA Tetraloops. The Journal of Physical Chemistry Letters. 7, 4032–4038 (2016)

[plumID:23.041] S. E. Hoff, F. E. Thomasen, K. Lindorff-Larsen, M. Bonomi, Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference (2023)

[plumID:23.031] F. P. Panei, P. Gkeka, M. Bonomi, Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN (2023)

[plumID:23.021] L. Leanza, C. Perego, L. Pesce, M. Salvalaglio, M. von Delius, G. M. Pavan, Into the dynamics of rotaxanes at atomistic resolution. Chemical Science. 14, 6716–6729 (2023)

[plumID:23.001] S. L. Bore, F. Paesani, Realistic phase diagram of water from “first principles” data-driven quantum simulations. Nature Communications. 14 (2023)

[plumID:22.037] B. Ashwood, M. S. Jones, A. L. Ferguson, A. Tokmakoff, Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site. Proceedings of the National Academy of Sciences. 120 (2023)

[plumID:22.027] Temmam S. et al. SARS-CoV-2-Related Bat Virus in Human Relevant Models Sheds Light on the Proximal Origin of COVID-19

[plumID:22.017] N. Ansari, V. Rizzi, M. Parrinello, Water regulates the residence time of Benzamidine in Trypsin. Nature Communications. 13 (2022)

[plumID:22.006] S. Hamsici, A. D. White, H. Acar, Peptide framework for screening the effects of amino acids on assembly. Science Advances. 8 (2022)

[plumID:21.049] A. Pérez de Alba Ortíz, B. Ensing. Simultaneous sampling of multiple transition channels using adaptive paths of collective variables

[plumID:21.039] L. Bonati, G. Piccini, M. Parrinello, Deep learning the slow modes for rare events sampling. Proceedings of the National Academy of Sciences. 118 (2021)

[plumID:21.029] Z. Smith, P. Tiwary, Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor Graphs. The Journal of Physical Chemistry B. 125, 11150–11158 (2021)

[plumID:21.019] N. F. Francia, L. S. Price, M. Salvalaglio, Reducing crystal structure overprediction of ibuprofen with large scale molecular dynamics simulations. CrystEngComm. 23, 5575–5584 (2021)

[plumID:21.009] K. M. Bal, Nucleation rates from small scale atomistic simulations and transition state theory. The Journal of Chemical Physics. 155 (2021)

[plumID:20.034] S. Bottaro, G. Bussi, K. Lindorff-Larsen, Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society. 143, 8333–8343 (2021)

[plumID:20.024] J. Debnath, M. Parrinello, Gaussian Mixture-Based Enhanced Sampling for Statics and Dynamics. The Journal of Physical Chemistry Letters. 11, 5076–5080 (2020)

[plumID:20.014] G. T. Heller, F. A. Aprile, T. C. T. Michaels, R. Limbocker, M. Perni, F. S. Ruggeri, B. Mannini, T. Löhr, M. Bonomi, C. Camilloni, A. De Simone, I. C. Felli, R. Pierattelli, T. P. J. Knowles, C. M. Dobson, M. Vendruscolo, Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease. Science Advances. 6 (2020)

[plumID:20.004] L. Bonati, V. Rizzi, M. Parrinello, Data-Driven Collective Variables for Enhanced Sampling. The Journal of Physical Chemistry Letters. 11, 2998–3004 (2020)

[plumID:19.078] F. Giberti, B. Cheng, G. A. Tribello, M. Ceriotti, Iterative Unbiasing of Quasi-Equilibrium Sampling. Journal of Chemical Theory and Computation. 16, 100–107 (2019)

[plumID:19.068] M. Invernizzi, M. Parrinello, Rethinking Metadynamics: From Bias Potentials to Probability Distributions. The Journal of Physical Chemistry Letters. 11, 2731–2736 (2020)

[plumID:19.058] V. Santolini, G. A. Tribello, K. E. Jelfs, Predicting solvent effects on the structure of porous organic molecules. Chemical Communications. 51, 15542–15545 (2015)

[plumID:19.048] G. Mattedi, F. Deflorian, J. S. Mason, C. de Graaf, F. L. Gervasio, Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. Journal of Chemical Information and Modeling. 59, 2830–2836 (2019)

[plumID:19.038] A. Achour, L. Broggini, X. Han, R. Sun, C. Santambrogio, J. Buratto, C. Visentin, A. Barbiroli, C. M. G. De Luca, P. Sormanni, F. Moda, A. De Simone, T. Sandalova, R. Grandori, C. Camilloni, S. Ricagno, Biochemical and biophysical comparison of human and mouse beta‐2 microglobulin reveals the molecular determinants of low amyloid propensity. The FEBS Journal. 287, 546–560 (2019)

[plumID:19.028] Y. Wang, J. M. L. Ribeiro, P. Tiwary, Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nature Communications. 10 (2019)

[plumID:19.018] C. Cozza, M. Bonomi, A. Pietropaolo, A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes. Journal of Chemical Theory and Computation. 14, 5441–5445 (2018)

[plumID:19.008] D. Trapl, I. Horvacanin, V. Mareska, F. Ozcelik, G. Unal, V. Spiwok, Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations. Frontiers in Molecular Biosciences. 6 (2019)

[plumID:24.004] Ziyue Zou, Pratyush Tiwary. Enhanced sampling of Crystal Nucleation with Graph Representation Learnt Variables.

[plumID:23.040] R. Capelli, G. Piccini, Atomistic Insights into Hydrogen-Bonded Supramolecular Capsule Self-Assembly Dynamics. The Journal of Physical Chemistry C. 128, 635–641 (2023)

[plumID:23.030] D. Ray, M. Parrinello, Data-driven classification of ligand unbinding pathways. Proceedings of the National Academy of Sciences. 121 (2024)

[plumID:23.020] M. Fortino, G. Schifino, D. Vitone, F. Arnesano, A. Pietropaolo, The stepwise dissociation of the Zn(II)-bound Atox1 homodimer and its energetic asymmetry. Inorganica Chimica Acta. 550, 121452 (2023)

[plumID:23.010] N. Saleh, P. Ibrahim, G. Saladino, F. L. Gervasio, T. Clark, An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. Journal of Chemical Information and Modeling. 57, 1210–1217 (2017)

[plumID:23.000] G. H. Zerze, P. M. Piaggi, P. G. Debenedetti, A Computational Study of RNA Tetraloop Thermodynamics, Including Misfolded States. The Journal of Physical Chemistry B. 125, 13685–13695 (2021)

[plumID:22.036] Z. Zhang, J. Šponer, G. Bussi, V. Mlýnský, P. Šulc, C. R. Simmons, N. Stephanopoulos, M. Krepl, Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of Chemical Information and Modeling. 63, 2794–2809 (2023)

[plumID:22.026] W. Yang, Y. Zhou, B. Jin, X. Qi, B. Cai, Q. Yin, J. Pfaendtner, J. J. De Yoreo, C.-L. Chen, Designing sequence-defined peptoids for fibrillar self-assembly and silicification. Journal of Colloid and Interface Science. 634, 450–459 (2023)

[plumID:22.016] P. M. Piaggi, J. Weis, A. Z. Panagiotopoulos, P. G. Debenedetti, R. Car, Homogeneous ice nucleation in an ab initio machine-learning model of water. Proceedings of the National Academy of Sciences. 119 (2022)

[plumID:22.005] V. Spiwok, M. Kurečka, A. Křenek, Collective Variable for Metadynamics Derived From AlphaFold Output. Frontiers in Molecular Biosciences. 9 (2022)

[plumID:21.048] E. Tao, B. Corry, Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors. Biophysical Journal. 121, 193–206 (2022)

[plumID:21.038] Z. Zou, S.-T. Tsai, P. Tiwary, Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. The Journal of Physical Chemistry B. 125, 13049–13056 (2021)

[plumID:21.028] E. Trizio, M. Parrinello, From Enhanced Sampling to Reaction Profiles. The Journal of Physical Chemistry Letters. 12, 8621–8626 (2021)

[plumID:21.018] Q. Zhao, R. Capelli, P. Carloni, B. Lüscher, J. Li, G. Rossetti, Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein–Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors. Journal of Chemical Theory and Computation. 17, 7899–7911 (2021)

[plumID:21.008] M. Fortino, C. Cozza, M. Bonomi, A. Pietropaolo, Multi-replica biased sampling for photoswitchable π-conjugated polymers. The Journal of Chemical Physics. 154 (2021)

[plumID:20.033] Z. F. Brotzakis, T. Löhr, M. Vendruscolo, Determination of intermediate state structures in the opening pathway of SARS-CoV-2 spike using cryo-electron microscopy. Chemical Science. 12, 9168–9175 (2021)

[plumID:20.023] D. Trapl, V. Spiwok, Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d. The R Journal. 14, 46–58 (2022)

[plumID:20.013] D. Trapl, C. C. del Río, P. Kříž, V. Spiwok, Prediction of pKa in a system with high orthogonal barriers: Alchemical flying Gaussian method. Chemical Physics Letters. 760, 138012 (2020)

[plumID:20.003] J. Debnath, M. Invernizzi, M. Parrinello, Enhanced Sampling of Transition States. Journal of Chemical Theory and Computation. 15, 2454–2459 (2019)

[plumID:19.077] J. Sampath, A. Kullman, R. Gebhart, G. Drobny, J. Pfaendtner, Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations. npj Computational Materials. 6 (2020)

[plumID:19.067] J. Rydzewski, R. Jakubowski, W. Nowak, H. Grubmüller, Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways. Journal of Chemical Theory and Computation. 14, 2843–2851 (2018)

[plumID:19.057] C. Paissoni, A. Jussupow, C. Camilloni, Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics. Journal of Chemical Theory and Computation. 16, 2825–2834 (2020)

[plumID:19.047] J. Pazúriková, A. Křenek, V. Spiwok, M. Šimková, Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. The Journal of Chemical Physics. 146 (2017)

[plumID:19.037] R. Drori, C. Li, C. Hu, P. Raiteri, A. L. Rohl, M. D. Ward, B. Kahr, A Supramolecular Ice Growth Inhibitor. Journal of the American Chemical Society. 138, 13396–13401 (2016)

[plumID:19.027] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle. Physical Review Letters. 122 (2019)

[plumID:19.017] R. Capelli, P. Carloni, M. Parrinello, Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics. The Journal of Physical Chemistry Letters. 10, 3495–3499 (2019)

[plumID:19.007] L. Eshun-Wilson, R. Zhang, D. Portran, M. V. Nachury, D. B. Toso, T. Löhr, M. Vendruscolo, M. Bonomi, J. S. Fraser, E. Nogales, Effects of α-tubulin acetylation on microtubule structure and stability. Proceedings of the National Academy of Sciences. 116, 10366–10371 (2019)

[plumID:23.039] E. R. Beyerle, P. Tiwary, Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation. The Journal of Physical Chemistry B. 128, 755–767 (2024)

[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)

[plumID:23.019] R. Bobrovs, L. Drunka, I. Kanepe, A. Jirgensons, A. Caflisch, M. Salvalaglio, K. Jaudzems, Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. Journal of Chemical Information and Modeling. 63, 6890–6899 (2023)

[plumID:23.009] D. Ray, E. Trizio, M. Parrinello, Deep learning collective variables from transition path ensemble. The Journal of Chemical Physics. 158 (2023)

[plumID:22.045] P. Falkenstein, Z. Zhao, A. Di Pede-Mattatelli, G. Künze, M. Sommer, C. Sonnendecker, W. Zimmermann, F. Colizzi, J. Matysik, C. Song, On the Binding Mode and Molecular Mechanism of Enzymatic Polyethylene Terephthalate Degradation. ACS Catalysis. 13, 6919–6933 (2023)

[plumID:22.035] M. A. Roesgaard, J. E. Lundsgaard, E. A. Newcombe, N. L. Jacobsen, F. Pesce, E. E. Tranchant, S. Lindemose, A. Prestel, R. Hartmann-Petersen, K. Lindorff-Larsen, B. B. Kragelund, Deciphering the Alphabet of Disorder—Glu and Asp Act Differently on Local but Not Global Properties. Biomolecules. 12, 1426 (2022)

[plumID:22.025] K. M. Bal, E. C. Neyts, Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory. The Journal of Chemical Physics. 157 (2022)

[plumID:22.015] J. Rydzewski, K. Walczewska-Szewc, S. Czach, W. Nowak, K. Kuczera, Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. The Journal of Physical Chemistry B. 126, 2647–2657 (2022)

[plumID:22.004] U. Raucci, V. Rizzi, M. Parrinello, Discover, Sample, and Refine: Exploring Chemistry with Enhanced Sampling Techniques. The Journal of Physical Chemistry Letters. 13, 1424–1430 (2022)

[plumID:21.047] P. M. Piaggi, O. Valsson, M. Parrinello, Erratum: Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations [Phys. Rev. Lett. 119 , 015701 (2017)]. Physical Review Letters. 125 (2020)

[plumID:21.037] S. Temmam, K. Vongphayloth, E. Baquero, S. Munier, M. Bonomi, B. Regnault, B. Douangboubpha, Y. Karami, D. Chrétien, D. Sanamxay, V. Xayaphet, P. Paphaphanh, V. Lacoste, S. Somlor, K. Lakeomany, N. Phommavanh, P. Pérot, O. Dehan, F. Amara, F. Donati, T. Bigot, M. Nilges, F. A. Rey, S. van der Werf, P. T. Brey, M. Eloit, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature. 604, 330–336 (2022)

[plumID:21.027] I. Galdadas, L. Carlino, R. A. Ward, S. J. Hughes, S. Haider, F. L. Gervasio, Structural basis of the effect of activating mutations on the EGF receptor. eLife. 10 (2021)

[plumID:21.017] S. Orioli, C. G. Henning Hansen, K. Lindorff-Larsen, Transient exposure of a buried phosphorylation site in an autoinhibited protein. Biophysical Journal. 121, 91–101 (2022)

[plumID:20.032] V. Marinova, L. Dodd, S.-J. Lee, G. P. F. Wood, I. Marziano, M. Salvalaglio, Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering. Journal of Chemical Information and Modeling. 61, 2263–2273 (2021)

[plumID:20.022] M. Invernizzi, P. M. Piaggi, M. Parrinello, Unified Approach to Enhanced Sampling. Physical Review X. 10 (2020)

[plumID:20.012] R. Evans, L. Hovan, G. A. Tribello, B. P. Cossins, C. Estarellas, F. L. Gervasio, Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies. Journal of Chemical Theory and Computation. 16, 4641–4654 (2020)

[plumID:20.002] L. S. M. Evenseth, R. Ocello, M. Gabrielsen, M. Masetti, M. Recanatini, I. Sylte, A. Cavalli, Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. Journal of Chemical Information and Modeling. 60, 2294–2303 (2020)

[plumID:19.076] S. Assenza, A. S. Sassi, R. Kellner, B. Schuler, P. De Los Rios, A. Barducci, Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. eLife. 8 (2019)

[plumID:19.066] J. Rydzewski, O. Valsson, Finding multiple reaction pathways of ligand unbinding. The Journal of Chemical Physics. 150 (2019)

[plumID:19.056] J. Rydzewski, maze: Heterogeneous ligand unbinding along transient protein tunnels. Computer Physics Communications. 247, 106865 (2020)

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[plumID:19.026] G. C. Sosso, T. F. Whale, M. A. Holden, P. Pedevilla, B. J. Murray, A. Michaelides, Unravelling the origins of ice nucleation on organic crystals. Chemical Science. 9, 8077–8088 (2018)

[plumID:19.016] P. Lucaioli, E. Nauha, I. Gimondi, L. S. Price, R. Guo, L. Iuzzolino, I. Singh, M. Salvalaglio, S. L. Price, N. Blagden, Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction. CrystEngComm. 20, 3971–3977 (2018)

[plumID:19.006] P. Kříž, Z. Šućur, V. Spiwok, Free-Energy Surface Prediction by Flying Gaussian Method: Multisystem Representation. The Journal of Physical Chemistry B. 121, 10479–10483 (2017)

[plumID:24.002] X. Wang, M. J. Servis, Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes. The Journal of Physical Chemistry B. 128, 263–272 (2023)

[plumID:23.028] M. Yang, U. Raucci, M. Parrinello, Reactant-induced dynamics of lithium imide surfaces during the ammonia decomposition process. Nature Catalysis. 6, 829–836 (2023)

[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)

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[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)

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[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)

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[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, A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations (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)

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[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)

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[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)

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[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)

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[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)

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[plumID:22.000] X. Lu, J. Huang, A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase. Communications Biology. 5 (2022)

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[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)

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[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)

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[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)