Bibliography

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

[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 et al., Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs, Frontiers in Molecular Biosciences 8 (2021)

[plumID:21.045] D. Maag et al., Electrostatic interactions contribute to the control of intramolecular thiol–disulfide isomerization in a protein, Physical Chemistry Chemical Physics (2021)

[plumID:21.043] H. Lu, J. Martí, Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes, (2021)

[plumID:21.042] X. Qi et al., Into the Facet-Selectivity of Sequenced Amphiphilic Peptoids at the Au-Water Interface, (2021)

[plumID:21.041] M. Badin, R. Martoňák, Nucleating a Different Coordination in a Crystal under Pressure: A Study of the B1−B2 Transition in NaCl by Metadynamics, Physical Review Letters 127 (2021)

[plumID:21.040] Z. F. Brotzakis, P. R. Lindstedt, R. Taylor, G. J. L. Bernardes, M. Vendruscolo, A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms, (2020)

[plumID:21.037] S. Temmam et al., Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula, (2021)

[plumID:21.033] A. Pérez de Alba Ortíz, J. Vreede, B. Ensing, Sequence dependence of transient Hoogsteen base-pairing in DNA, (2021)

[plumID:21.029] Z. Smith, P. Tiwary, Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs, (2021)

[plumID:21.027] I. Galdadas et al., Structural basis of the effect of activating mutations on the EGF receptor, eLife 10 (2021)

[plumID:21.025] Y. Karami et al., Computational and biochemical analysis of type IV Pilus dynamics and stability, (2021)

[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:21.021] 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 et al., An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADP-ribosylation hydrolases inhibitors, (2021)

[plumID:21.017] S. Orioli, C. G. Henning Hansen, K. Lindorff-Larsen, Transient exposure of a buried phosphorylation site in an autoinhibited protein, (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:21.015] E. Madland et al., NMR structures and functional roles of two related chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus, (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:21.011] 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:21.005] 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:21.002] 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 et al., 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 et al., 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 et al., 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, P. Garriga, Ed. 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:20.022] M. Invernizzi, P. M. Piaggi, M. Parrinello, Unified Approach to Enhanced Sampling, Physical Review X 10 (2020)

[plumID:20.021] E. Karlsson et al., 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 et al., Structural basis for stereospecific inhibition of ASCT2 from rational design, (2020)

[plumID:20.014] G. T. Heller et al., 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 et al., 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 et al., The dynamics of linear polyubiquitin, Science Advances 6 (2020)

[plumID:20.008] K. Rossi et al., 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 et al., 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 et al., 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 et al., Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution, Biophysical Journal 119, 978–988 (2020)

[plumID:20.000] R. Capelli et al., 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 et al., 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 et al., 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 et al., 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 et al., 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 et al., Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations, Scientific Reports 8 (2018)

[plumID:19.034] A. Pérez de Alba Ortíz, A. Tiwari, R. C. Puthenkalathil, B. Ensing, Advances in enhanced sampling along adaptive paths of collective variables, The Journal of Chemical Physics 149, 072320 (2018)

[plumID:19.033] A. Pérez de Alba Ortíz, A. Tiwari, R. C. Puthenkalathil, B. Ensing, Advances in enhanced sampling along adaptive paths of collective variables, The Journal of Chemical Physics 149, 072320 (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:19.029] P. Marinelli et al., 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 et al., 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 et al., 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:19.018] 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 et al., 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 et al., 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 et al., 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)

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