Bibliography

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

[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 (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:22.023] 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:22.021] S. L. Bore, P. M. Piaggi, R. Car, F. Paesani, Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations (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:22.019] R. Bobrovs, E. Basens, L. Drunka, I. Kanepe, S. Matisone, K. Velins, V. Andrianov, G. Leitis, D. Zelencova-Gopejenko, D. Rasina, A. Jirgensons, K. Jaudzems, Exploring aspartic protease inhibitor binding to design selective antimalarials (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 (2022)

[plumID:22.017] N. Ansari, V. Rizzi, M. Parrinello. Water regulates the residence time of Benzamidine in Trypsin.

[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

[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:22.014] 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:22.013] 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:22.011] S. Mehdi, D. Wang, S. Pant, P. Tiwary. Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck.

[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: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: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: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:22.005] V. Spiwok, M. Kurečka, A. Křenek, Collective Variable for Metadynamics Derived From AlphaFold Output. Frontiers in Molecular Biosciences. 9 (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: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: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:22.001] B. Pampel, O. Valsson. Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.

[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:21.051] 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 (2022)

[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 (2021)

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

[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:21.047] 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:21.046] 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:21.045] 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:21.044] A. R. Finney, M. Salvalaglio, Multiple pathways in NaCl homogeneous crystal nucleation. Faraday Discussions (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:21.042] 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:21.041] 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:21.040] 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:21.039] 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:21.038] 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:21.037] 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:21.036] 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:21.035] 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:21.034] 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:21.033] 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:21.032] 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:21.031] 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:21.030] 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:21.029] 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:21.028] E. Trizio, M. Parrinello, From Enhanced Sampling to Reaction Profiles. The Journal of Physical Chemistry Letters. 12, 8621–8626 (2021)

[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:21.026] F. Colizzi, M. Orozco, Probing allosteric regulations with coevolution-driven molecular simulations. Science Advances. 7 (2021)

[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:21.024] 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:21.023] 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:21.022] 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:21.021] 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:21.020] 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:21.019] 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:21.018] 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:21.017] 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: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:21.015] 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:21.014] C. Paissoni, C. Camilloni, How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case. Frontiers in Molecular Biosciences. 8 (2021)

[plumID:21.013] 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:21.012] 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:21.011] 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:21.010] 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:21.009] K. M. Bal, Nucleation rates from small scale atomistic simulations and transition state theory. The Journal of Chemical Physics. 155, 144111 (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:21.006] M. Invernizzi, OPES: On-the-fly Probability Enhanced Sampling method, Il Nuovo Cimento C 4, 112 (2021)

[plumID:21.005] T. Karmakar, M. Invernizzi, V. Rizzi, M. Parrinello, Collective variables for the study of crystallisation. Molecular Physics. 119 (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: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: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: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: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:20.034] 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:20.033] 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:20.032] 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:20.031] 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:20.030] 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:20.029] 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:20.028] 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:20.027] 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:20.026] 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:20.025] V. Rizzi, L. Bonati, N. Ansari, M. Parrinello, The role of water in host-guest interaction. Nature Communications. 12 (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:20.023] D. Trapl, V. Spiwok. Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

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

[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:20.020] 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:20.019] 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:20.018] 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:20.017] 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:20.016] 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:20.015] 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:20.014] 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:20.013] 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:20.012] 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:20.011] 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:20.010] 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:20.009] 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: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: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: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: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: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:20.003] J. Debnath, M. Invernizzi, M. Parrinello, Enhanced Sampling of Transition States. Journal of Chemical Theory and Computation. 15, 2454–2459 (2019)

[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: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: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:19.083] 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:19.082] 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:19.081] P. M. Piaggi, M. Parrinello, Calculation of phase diagrams in the multithermal-multibaric ensemble. The Journal of Chemical Physics. 150, 244119 (2019)

[plumID:19.080] 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:19.079] 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:19.078] 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:19.077] 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:19.076] 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:19.075] 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:19.074] 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:19.073] 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:19.072] 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:19.071] V. Marinova, M. Salvalaglio, Time-independent free energies from metadynamics via mean force integration. The Journal of Chemical Physics. 151, 164115 (2019)

[plumID:19.070] 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:19.069] 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:19.068] M. Invernizzi, M. Parrinello, Rethinking Metadynamics: From Bias Potentials to Probability Distributions. The Journal of Physical Chemistry Letters. 11, 2731–2736 (2020)

[plumID:19.067] 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:19.066] J. Rydzewski, O. Valsson, Finding multiple reaction pathways of ligand unbinding. The Journal of Chemical Physics. 150, 221101 (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:19.064] J. Sampath, J. Pfaendtner, Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Molecular Physics. 117, 3642–3650 (2019)

[plumID:19.063] 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:19.062] J. Smith, P. McMullen, Z. Yuan, J. Pfaendtner, S. Jiang, Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules. 21, 435–443 (2019)

[plumID:19.061] 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:19.060] 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:19.058] 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:19.057] 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:19.056] J. Rydzewski, maze: Heterogeneous ligand unbinding along transient protein tunnels. Computer Physics Communications. 247, 106865 (2020)

[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:19.054] G. Piccini, M. Parrinello, Accurate Quantum Chemical Free Energies at Affordable Cost. The Journal of Physical Chemistry Letters. 10, 3727–3731 (2019)

[plumID:19.053] 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:19.052] 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:19.051] B. Cheng, G. A. Tribello, M. Ceriotti, Solid-liquid interfacial free energy out of equilibrium. Physical Review B. 92 (2015)

[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:19.049] 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:19.048] 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:19.047] 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:19.046] 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:19.045] 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:19.044] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle. Physical Review Letters. 122 (2019)

[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:19.042] D. Mendels, G. Piccini, M. Parrinello, Collective Variables from Local Fluctuations. The Journal of Physical Chemistry Letters. 9, 2776–2781 (2018)

[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:19.040] 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:19.039] 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:19.038] 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:19.037] 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:19.036] 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:19.035] 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:19.032] 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:19.031] 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:19.029] 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:19.028] 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:19.027] P. M. Piaggi, M. Parrinello, Multithermal-Multibaric Molecular Simulations from a Variational Principle. Physical Review Letters. 122 (2019)

[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:19.025] 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:19.024] 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:19.023] 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:19.022] 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:19.021] G. M. Hocky, T. Dannenhoffer-Lafage, G. A. Voth, Coarse-Grained Directed Simulation. Journal of Chemical Theory and Computation. 13, 4593–4603 (2017)

[plumID:19.020] 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:19.019] 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:19.018] 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:19.017] 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:19.016] 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:19.015] 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:19.014] 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:19.013] 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:19.012] 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:19.011] 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:19.010] 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:19.009] 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: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: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: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: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:19.004] M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo, Metainference: A Bayesian inference method for heterogeneous systems. Science Advances. 2 (2016)

[plumID:19.003] S. Vahidi, Z. A. Ripstein, M. Bonomi, T. Yuwen, M. F. Mabanglo, J. B. Juravsky, K. Rizzolo, A. Velyvis, W. A. Houry, M. Vendruscolo, J. L. Rubinstein, L. E. Kay, Reversible inhibition of the ClpP protease via an N-terminal conformational switch. Proceedings of the National Academy of Sciences. 115 (2018)

[plumID: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: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: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)