Bibliography

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

[plumID:22.041] M. Invernizzi, A. Krämer, C. Clementi, F. Noé. Skipping the replica exchange ladder with normalizing flows

[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, 054504 (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: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, 114118 (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, 104707 (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: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, Hydrogen Bond Synchronized Dual Activation Enables the Unified β-Selective O-Glycosylation Inside a Molecular Capsule (2021)

[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, 244120 (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, 244119 (2019)

[plumID:19.071] V. Marinova, M. Salvalaglio, Time-independent free energies from metadynamics via mean force integration. The Journal of Chemical Physics. 151, 164115 (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:22.039] Z. Zou, E. Beyerle, S-T. Tsai, P. Tiwary. Driving and characterizing nucleation of urea and glycine polymorphs in water

[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, 154301 (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: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. C. Ciacchi, Exploration, representation and rationalization of the conformational phase-space of N-glycans (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 (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] M. Zhao, K. J. Lachowski, S. Zhang, S. Alamdari, J. Sampath, P. Mu, C. J. Mundy, J. Pfaendtner, J. J. De Yoreo, C.-L. Chen, L. D. Pozzo, A. L. Ferguson, Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets. Biomacromolecules. 23, 992–1008 (2022)

[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, 072309 (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: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.

[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, 144111 (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: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, 174108 (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 (2021)

[plumID:20.023] D. Trapl, V. Spiwok. Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

[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, 115101 (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: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 (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, 184113 (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, 221101 (2019)

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

[plumID:19.046] Z. F. Brotzakis, V. Limongelli, M. Parrinello, Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables. Journal of Chemical Theory and Computation. 15, 743–750 (2018)

[plumID:19.036] D. Meral, D. Provasi, M. Filizola, An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber. The Journal of Chemical Physics. 149, 224101 (2018)

[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: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, 165102 (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:22.033] I. Kolossváry, W. Sherman, A Different Kind of Restraint Suitable for Molecular Dynamics Simulations (2022)

[plumID:22.023] Z. F. Brotzakis, T. Löhr, S. Truong, S. E. 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 (2022)

[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, 204116 (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)

[plumID:22.032] I. Kolossváry, W. Sherman, A Different Kind of Restraint Suitable for Molecular Dynamics Simulations (2022)

[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, 2000092 (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)