Browse the nest

PLUMED-NEST provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation or analysis contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual.

Here is the list of projects already deposited in PLUMED-NEST, while a complete bibliography can be found here.

plumID Name Category Keywords Contributor
23.045 Minute-timescale simulations of G Protein Coupled Receptor A2A activation mechanism reveal a receptor pseudo-active state bio Path CVs Metadynamics, GPCRs activation transition Limongelli V.
23.034 Urea nucleation in water: do long-range forces matter? materials LMF theory, Metadynamics, Nucleation Zou Z.
23.024 Permutationally Invariant Networks for Enhanced Sampling (PINES) methods collective variables, enhanced sampling, data-driven, deep learning, permutational invariance, solvent Herringer N.
23.014 Structural basis of dimerization of chemokine receptors CCR5 and CXCR4 bio metadynamics, oligomerization, chemokine receptors, GPCR, membrane Limongelli V.
23.004 Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point chemistry water, liquid-liquid transition, second critical point, ice, polymorphs, melting curves, environment similarity, opes, density-functional theory, scan, machine learning potential Piaggi P.
22.040 From Closed to Open. Omicron Mutations Increase Interdomain Interactions and Reduce Epitope Exposure bio SARS-CoV-2, Spike, Omicron Wieczór M.
22.030 Mixing physics across temperatures with generative artificial intelligence methods REMD, Generative AI, DDPM Wang Y.
22.020 Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA bio RNA force field, Helix-Junction-Helix RNA, SAXS, Well tempered metadynamics He W.
22.009 Glycosylation in calixarenes capsule chemistry Metadynamics, glycosylation, supramolecular catalysis Piccini G.
21.052 On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets materials Ibuprofen, unbinding, WTmetaD Salvalaglio M.
21.042 Peptoid-mediated Au nanocrystal growth materials parallel-bias metadynamics, peptoid, Au Qi X.
21.032 Metal-coupled folding mechanism to metallothionein bio parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination Diaz M.
21.022 Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly materials parallel bias metadynamics, adsorption, peptide Qi X.
21.012 NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition bio funnel metadynamics Pfaendtner J.
21.002 Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional materials ice, water, SCAN, OPES, VES, multithermal, crystallization, environment similarity, refcv, reweighting Piaggi P.
20.027 Allosteric Regulation of SARS-CoV-2 Protease. Towards Informed Structure-Based Drug Discovery bio SARS-CoV2, MPro, Covid-19, Molecular Dynamics, Metadynamics, Computer-Aided Drug Discovery Abdel-Maksoud K.
20.017 FISST methods FISST, force, peptide, sampling, tempering Hocky G.
20.007 Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics bio metadynamics, loop movement, artificial intelligence Tiwary P.
19.081 Calculation of phase diagrams in the multithermal-multibaric ensemble methods VES, variationally enhanced sampling, multithermal-multibaric, energy, Wang Landau, RefCV, kernel, bcc, fcc, sodium, aluminum Piaggi P.
19.071 Time-independent free energies from metadynamics via Mean Force Integration methods metadynamics, mean force integration, MFI, thermodynamic integration Salvalaglio M.
19.061 Diffusion in porous materials materials metadynamics, porous materials, diffusion Jelfs K.
19.051 Solid liquid interfacial free energy out of equilibrium materials metadynamics, nucleation, surface excess free energy Tribello G.
19.041 Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces bio metadynamics, collective variables, conformational changes, multiple walkers, Well-Tempered MetaD, peptide, binding, phosphorylation, post-transitional motif, sio2, adsorption Pfaendtner J.
19.031 Ice nucleation using PIV-based path coordinates materials phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics Pipolo S.
19.021 Coarse-Grained Directed Simulation methods experiment directed simulation, coarse-grain, bias Hocky G.
19.011 Automatic Gradient Computation for Collective Variables other gradient, differentiation, curvature Giorgino T.
19.001 RNA SHAPE bio metadynamics, RNA, ligand binding Bussi G.
23.044 Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition materials metadynamics, interlocked molecules Leanza L.
23.033 DNA G-quadruplex and G-hairpin folding with ST-metaD protocol bio DNA, G4, GQ, quadruplex, hairpin, folding, metadynamics, REST2, ST-metaD Pokorná P.
23.023 Rational design of novel biomimetic sequence-defined polymers for mineralization applications methods metadynamics, surface binding, biomimetic mineralization Torkelson K.
23.013 Path meta-eABF simulation of large scale conformational change in STING protein methods meta-eABF, path CV, large scale conformational change, STING protein, reciprocal barrier restraint Kolossvary I.
23.003 Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations methods metadynamics, alchemical variable, alchemical free energy calculations Hsu W.
22.039 Driving and characterizing nucleation of urea and glycine polymorphs in water bio metadynamics, nucleation, amino acids, polymorphism Beyerle E.
22.029 Angiotensin-1-7_Metadynamics bio Metadynamics, Angiotensin-(1-7), peptide Chi L.
22.019 Exploring aspartic protease inhibitor binding to design selective antimalarials bio ligand binding, loop opening, path CV, funnel metadynamics, drug development Bobrovs R.
22.008 Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters materials Well tempered metadynamics, ab-initio, ase Sucerquia D.
21.051 Automatic learning of hydrogen-bond fixes in an AMBER RNA force field methods force field, RNA Bussi G.
21.041 Nucleating a Different Coordination in a Crystal under Pressure. A Study of the B1−B2 Transition in NaCl by Metadynamics methods metadynamics, structural phase transitions, pressure-induced phase transition, martensitic transitions Badin M.
21.031 Photo-switchable sulfonulureas in KATP channel bio metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels Walczewska-Szewc K.
21.021 ATLAS methods Machine Learning, Metadynamics Giberti F.
21.011 CmuMD simulations of NaCl(aq) at graphite chemistry CmuMD, DFS clustering Finney A.
21.001 Substrate recognition and catalysis by glycosaminoglycan sulfotransferases bio metadynamics, well-tempered metadynamics, puckering, coordination Ferreira T.
20.026 Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor bio Metadynamics, Umbrella sampling Peters B.
20.016 Predicting polymorphism in molecular crystals using orientational entropy materials metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy Piaggi P.
20.006 Class B GPCR activation mechanism bio metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F.
19.080 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium methods ves, variationally enhanced sampling, vibrational excitation, chemical reactions Bal K.
19.070 Unexpected Dynamics in the UUCG RNA Tetraloop bio well-tempered metadynamics, RNA, UUCG, maximum entropy Bottaro S.
19.060 Neural networks-based variationally enhanced sampling methods ves, neural networks Bonati L.
19.050 Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes chemistry metadynamics, membranes, Willard Chandler surface Tribello G.
19.040 Optimal Metric for Path Collective Variables bio metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path Gervasio F.
19.030 Coarse-Grained MetaDynamics (CG-MetaD) bio Coarse-grained, metadynamics, protein-protein interaction, protein-protein binding free energy Limongelli V.
19.020 PTMetaD-WTE simulation of the Ntail IDP bio metadynamics, IDPs, protein folding Bernetti M.
19.010 Multi-domain protein dynamics bio metainference, NMR, protein dynamics Camilloni C.
19.000 VesDeltaF methods VES, convergence, suboptimal CVs Invernizzi M.
23.043 Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling materials Barium Titanate, ferroelectric phase transition, Machine Learning, polarization order parameters Gigli L.
23.032 Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics bio metadynamics, tSNE, neural network, machine learning, trp-cage, folding Spiwok V.
23.022 A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar methods collective variables, machine learning, toy model Trizio E.
23.012 JAK2 2D meta-eABF PMF with statistical analysis bio 2D meta-eABF, path CV, PMF Kolossvary I.
23.002 Critical comparison of general-purpose collective variables for crystal nucleation methods metadynamics, umbrella sampling, commitor, entropy, PIV Lam J.
22.038 Enhanced Sampling Aided Design of Molecular Photoswitches chemistry reaction discovery, OPES explore, graph CV Raucci U.
22.028 N-glycan conformer distributions in atomistic simulation bio REST2, RECT, N-glycan, pucker Grothaus I.
22.018 Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations bio ligand binding, docking, EMMI, LAT1 Bonomi M.
22.007 Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy bio metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy Papaleo E.
21.050 N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity methods bio Grothaus I.
21.040 A structural ensemble of a tau-microtubule complex reveals regulatory tau phosphorylation and acetylation mechanisms bio EMMI, CryoEM, tau-microtubules, post-translational modifications, chemical mutagenesis, structural ensemble, Metainference Brotzakis F.
21.030 Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains bio parallel bias parallel tempered metadynamics in WTE, synthetic foldamers, self-assembly, peptoid secondary structure Pfaendtner J.
21.020 Reweighted Jarzynski sampling methods free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions Bal K.
21.010 Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry chemistry Strecker reaction, free energy landscape, ab initio molecular dynamics, glycine, prebiotic synthesis Magrino T.
21.000 Uremic toxin time scale dynamics bio uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs) Pfaendtner J.
20.025 The role of water in host-guest interaction bio ligand binding, water, opes, SAMPL5 Rizzi V.
20.015 Rational design of ASCT2 inhibitors using an integrated experimental-computational approach bio ASCT2 transporter, small-molecules, cryo-EM, metainference Bonomi M.
20.005 Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations bio Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD Capelli R.
19.079 Impact of Glutamate Carboxylation in the Adsorption of the alpha-1 Domain of Osteocalcin to Hydroxyapatite and Titania bio metadynamics, peptide adsorption, parallel tempering, well-tempered ensemble Alamdari S.
19.069 Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen materials ibuprofen, crystal, solvent, surface Salvalaglio M.
19.059 cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide bio bias-exchange metadynamics, cis-trans isomerization Marinelli F.
19.049 Determining the sizes of solid/liquid clusters in MD trajectories of nucleation methods nucleation, metadynamics, clustering, Steinhardt order parameters Tribello G.
19.039 Funnel Metadynamics bio funnel-metadynamics, absolute binding free energy, ligand-receptor complexes Limongelli V.
19.029 WTE-metaD of FF domain of URNF1 C57D variant bio metadynamics, mutations, post-translational modification, ff domain Papaleo E.
19.019 FA-MetaD-JCP-Wang-et-al bio Frequency adaptive metadynamics; peptide Lindorff-Larsen K.
19.009 RNA tetraloops folding bio metadynamics, RNA, folding Bussi G.
23.041 Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference methods EMMIVox, cryo-EM, single-structure refinement, ensemble refinement, Bayesian inference, B-factors, structural ensembles Hoff S.
23.031 Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN bio RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites Bonomi M.
23.021 Into the Dynamics of Rotaxanes at Atomistic Resolution materials metadynamics, rotaxanes, molecular shuttles, molecular machines Leanza L.
23.011 OneOPES, a combined enhanced sampling method to rule them all bio OPES, Replica Exchange, Multithermal, Ligand Binding, Protein Folding Rizzi V.
23.001 Quantum phase diagram of water chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S.
22.037 Splitting of Energetic and Dynamics Base Pairing Cooperativity in DNA Duplexes by an Abasic Site chemistry metadynamics, DNA, abasic Jones M.
22.027 Molecular Dynamics simulations of BANAL-236 RBD-hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, BANAL-236, receptor-binding domain Bonomi M.
22.017 Water regulates the residence time of Benzamidine in Trypsin bio ligand binding, water, opes, benzamidine trypsin, unbinding rates, machine learning, Deep-LDA, Deep-TICA Ansari N.
22.006 Peptide framework for screening the effects of amino acids on assembly bio metadynamics, peptides White A.
21.049 Multiple-path-metadynamics and PathMaps methods path-CV, metadynamics, multiple-walker, multiple paths, pathmap Pérez-de-Alba-Ortíz A.
21.039 Deep learning the slow modes for rare events sampling methods collective variables, machine learning, slow modes, deep-tica, opes Bonati L.
21.029 Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs bio metadynamics, small peptide, machine learning Tiwary P.
21.019 Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations materials Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen Salvalaglio M.
21.009 Nucleation rates from small scale atomistic simulations and transition state theory materials kinetics, free energy barriers, nucleation, droplets, metadynamics Bal K.
20.034 Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations bio RNA, SARS-CoV-2, partial tempering Bottaro S.
20.024 Gaussian Mixture Based Enhanced Sampling (GAMBES) methods enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias Debnath J.
20.014 amyloid beta small molecule interaction bio intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta Heller G.
20.004 Data-driven collective variables for enhanced sampling methods collective variables, machine learning, deep-lda Bonati L.
19.078 Iterative unbiasing of quasi-equilibrium sampling methods metadynamics, reweighting Giberti F.
19.068 Rethinking Metadynamics methods metadynamics, opes, convergence Invernizzi M.
19.058 Constrained MD for maintaining a cavity in a calculation chemistry constrained MD, porous molecules, porosity, cavity Jelfs K.
19.048 Understanding Ligand Binding Selectivity in a Prototypical GPCR Family bio metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding Gervasio F.
19.038 native state dynamics of human and mouse b2m bio metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation Camilloni C.
19.028 pRAVE methods RAVE, reaction coordinate, deep learning, metadynamics, kinetics Tiwary P.
19.018 Excited state FEP/Metadynamics simulations chemistry metadynamics, FEP, excited states, conjugated polymers, torsional potential Pietropaolo A.
19.008 anncolvar methods neural network, dimensionality reduction Spiwok V.
23.040 Supramolecular capsules assembly dynamics chemistry Self-assembly, H-bond capsules, resorcinarene, pyrogallolarene, metadynamics Capelli R.
23.030 Data Driven Classification of Ligand Unbinding Pathways bio OPES Explore, OPES Flooding, Benzene T4 Lysozyme, Ligand unbinding, Pathway classification, Kinetics, Residence time Ray D.
23.020 FEP simulations of ATOX1 homodimer chemistry parallel bias metadynamics, FEP, free-energy of metal ion dissociation Pietropaolo A.
23.010 An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G‑Protein-Coupled Receptor Ligands bio GPCR, binding free energy, free energy surface Clark T.
23.000 Atomistic simulations of RNA tetraloop folding via PTWTE-WTM bio parallel tempering, well-tempered metadynamics, well-tempered ensemble, RNA, Tetraloop, Folding Zerze G.
22.036 Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction bio Well-tempered MetaDynamics with Hamiltonian Replica Exchange Krepl M.
22.026 Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification materials Peptoid, silica Pfaendtner J.
22.016 Homogeneous ice nucleation in an ab initio machine learning model of water chemistry ice, water, nucleation, seeding, environment similarity, interfacial free energy, interfaces Piaggi P.
22.005 Collective Variable for Metadynamics Derived from AlphaFold Output bio AlphaFold, protein folding, protein structure prediction, metadynamics, deep learning, free energy simulation, collective variable Spiwok V.
21.048 Enhancing ligand exploration within a channel pore and fenestrations using metadynamics bio well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug Tao E.
21.038 Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics materials metadynamics, SGOOP, nucleation, urea Zou Z.
21.028 From Enhanced Sampling to Reaction Profiles methods collective variables, multi-state, machine learning, Deep-TDA Trizio E.
21.018 Localized Volume-based Metadynamics bio LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification Capelli R.
21.008 Multi-replica biased sampling for photoisomerization processes in conjugated polymers methods metadynamics, FEP, replica-exchange Pietropaolo A.
20.033 COVID-19 Spike protein opening transition mechanism bio EMMI, CryoEM, COVID-19, Spike, Metainference Brotzakis F.
20.023 metadynminer and metadynminer3d methods metadynamics, visualization, R Spiwok V.
20.013 Improving accuracy of biased Alchemistic simulations methods flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting Spiwok V.
20.003 Enhanced sampling of transition states methods Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction Debnath J.
19.077 Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations materials metadynamics, peptide-surface binding Pfaendtner J.
19.067 Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways bio metadynamics, ligand unbinding Rydzewski J.
19.057 SAXS ensembles using Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics Paissoni C.
19.047 Close Structure methods metadynamics, RMSD, path collective variables, property map Spiwok V.
19.037 Scission free energy of organic dyes chemistry metadynamics, multiple walkers, matheval/lepton Raiteri P.
19.027 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, liquid sodium, density anomaly Piaggi P.
19.017 Ligand binding pathways exploration bio metadynamics, ligand binding Capelli R.
19.007 EMMI Microtubules bio metainference, cryo-EM Bonomi M.
23.039 Thermodynamically inspired machine-learned reaction coordinates for hydrophobic ligand dissociation chemistry metadynamics, ligand dissociation Beyerle E.
23.029 An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations bio SAXS, SANS, SAS, metainference, proteins, nucleic-acid Ballabio F.
23.019 Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors bio binding pathway, binding energy, sketch-map, drug development Bobrovs R.
23.009 Deep Learning Collective Variables from Transition Path Ensemble methods TPI-Deep-TDA, Deep-TDA, Transition Path, OPES, OPES Flooding, Machine Learning, Protein folding, Ligand binding Ray D.
22.045 Binding mode and mechanism of enzymatic polyethylene terephthalate degradation bio metadynamics, TfCut2, PET, HREX, enzymatic polyethylene terephthalate degradation Colizzi F.
22.035 Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties bio intrinsically disordered proteins, parallel bias metadynamics, protein Lindorff-Larsen K.
22.025 Bubble nucleation rate predictions in a Lennard-Jones fluid materials free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation Bal K.
22.015 Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome bio photodynamics, bacteriophytochrome, variationally enhanced sampling Rydzewski J.
22.004 Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques chemistry reaction discovery, OPES, collective variables Raucci U.
21.047 Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations materials pair entropy, metadynamics, ves, solids, crystallization Piaggi P.
21.037 Molecular Dynamics simulations of RBD/hACE2 complexes bio SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain Bonomi M.
21.027 EGFR activating mutations mechanism bio metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA Gervasio F.
21.017 All-atom simulations of the Vav1 AD construct bio metadynamics, parallel-bias, well-tempered Orioli S.
21.007 Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling bio metadynamics, machine learning, protein folding Spiwok V.
20.032 Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil materials clustering, conformational isomers Salvalaglio M.
20.022 Unified Approach to Enhanced Sampling methods OPES, expanded ensembles, importance sampling Invernizzi M.
20.012 Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies bio metadynamics, well-tempered ensemble, ligand binding, binding affinity calculations, novel COLVAR, funnel restraints, Hamiltonian replica-exchange, PathCV, COMetPath, SWISH Gervasio F.
20.002 Exploring conformational dynamics of the extracellular Venus flytrap domain of the GABAB receptor, a path-metadynamics study bio Metadynamics, path CVs Ocello R.
19.076 Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones bio molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics Assenza S.
19.066 Finding ligand unbinding reaction pathways methods maze, ligand unbinding Rydzewski J.
19.056 maze methods maze, ligand unbinding Rydzewski J.
19.036 Thermodynamics and kinetics of G protein-coupled receptor activation bio metadynamics, allostery, receptor conformation, GPCR, pharmacology Provasi D.
19.026 Ice Nucleation on Cholesterol Crystals materials forward flux sampling, crystal nucleation, water, ice, organic crystals Sosso G.
19.016 Succinnic acid gamma polymorph materials Succinnic acid, conformers, polymorphs, metadynamics Salvalaglio M.
19.006 Flying Gaussian proof methods flying Gaussians, alanine dipeptide Spiwok V.
23.038 Determinants of Neutral Antagonism and Inverse Agonism in the β2-adrenergic receptor bio protein coupled receptor, beta-adrenergic, receptor activation, antagonism, inverse agonism, metadynamics Clark T.
23.028 Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process chemistry Ammonia decomposition; Dynamics;OPES; Neural Network potential Yang M.
23.018 Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention materials metadynamics, surface binding, peptide adsorption Torkelson K.
23.008 PBMetaD simulations of Histatin5 bio metadynamics, IDP, Rg, PPII Pesce F.
22.044 Colloid Crystallisation Analyses materials Q4, Q6, Pair Entropy, DFS Finney A.
22.034 Rationalising the difference in crystallisability of two Sulflowers using efficient in silico methods materials metadynamics, crystallizability, crystal structure prediction, sulflower, persulforated coronene Salvalaglio M.
22.024 Conformational Entropy as a Potential Liability of Computationally Designed Antibodies bio metadynamics, conformational entropy, antibody, nanobody Löhr T.
22.014 Quasi Liquid Layer Order Parameters materials Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint Shi J.
22.003 Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling methods opes, metadynamics, reweighting, alanine, muller Invernizzi M.
21.046 Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs bio wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder Papaleo E.
21.036 Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations bio Bias Exchange Metadynamics, PTWTE-metaD Salvalaglio M.
21.026 Probing allosteric regulations with coevolution-driven molecular simulations bio metadynamics, coevolution, allostery, adenylate cyclase Colizzi F.
21.016 MD SAXS GTPase associated center bio metadynamics, RNA, folding, SAXS Bussi G.
21.006 OPES, On-the-fly Probability Enhanced Sampling Method methods opes, alanine dipeptide, well-tempered, multithermal, multiumbrella Invernizzi M.
20.031 Soft fluorescent nanoshuttles targeting receptors chemistry polymers, receptors, nanoparticles, fluorescent probes Pietropaolo A.
20.021 Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. bio phi-values, restrained MD, transition-state, protein folding, disordered proteins, protein evolution Paissoni C.
20.011 Uremic toxin analysis bio metadynamics, uremic toxin, serum albumin Pfaendtner J.
20.001 Conformational stability and dynamics in solution and in crystals report similarly on unfolding and aggregation propensity of amyloidogenic proteins bio metainference, metadynamics, NMR, protein dynamics, b2m, protein crystals Camilloni C.
19.075 PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python other Python, automatic differentiation Giorgino T.
19.065 Molecular Enhanced Sampling with Autoencoders methods enhanced sampling, collective variables, deep learning Chen W.
19.055 Flying Gaussian method methods flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin Spiwok V.
19.045 Adsorption free energy of Ca/CO3 ions on calcite steps in contact with water materials metadynamics, well-tempered, multiple walkers, LAMMPS Pierre M.
19.035 Dimerization of GPCRs from coarse-grained umbrella sampling bio Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization Provasi D.
19.025 Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide bio metainference, NMR, protein dynamics, force-fields Camilloni C.
19.015 Ibuprofen conformational dynamics and thermodynamics surface materials Ibuprofen, crystal, surface, solvents, conformers, metadynamics Salvalaglio M.
19.005 Cmyc small molecule interaction bio metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP Heller G.
23.037 Estimating binding free energy of solid binding peptides without extensive sampling bio metadynamics, solid binding peptides Qi X.
23.027 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, DFS, Q3, Pair Entropy Finney A.
23.017 How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques bio enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV Das S.
23.007 Origins of Conformational Heterogeneity in Peptoid Helices formed by Chiral N-1-Phenylethyl Sidechains bio metadynamics, peptoids, parallel-bias metadynamics Pfaendtner J.
22.043 Atomistic simulations of RNA tetraloop folding via expanded ensemble OPES bio OPES, RNA, Tetraloop, Folding Zerze G.
22.033 Reciprocal barrier restraint. Application to PROTAC passive permeability prediction methods PROTAC, membrane permeability, PMF, restraint, meta-eABF, metadynamics, DRR Kolossvary I.
22.023 Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy bio CryoEM, MEMMI,EMMI, Metadynamics, Metainference, IAPP, structural ensemble Brotzakis F.
22.013 Ligand dissociation from PreQ1 riboswitch bio ligand, RNA, metadynamics, pRAVE Wang Y.
22.002 GAMBES_SAMPL5_RATES other GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding Debnath J.
21.045 QM/MM metadynamics of thiol-disulfide exchange between methylthiolate and dimethyldisulfide in water with an imposed external electrostatic potential (ESP) chemistry metadynamics, QM/MM, electrostatic potential, thiol-disulfide exchange Maag D.
21.035 CmuMD simulations of NaCl(aq) at NaCl chemistry CmuMD, interface Finney A.
21.025 Computational and biochemical analysis of type IV pilus dynamics and stability bio molecular dynamics, calcium binding, Type IV pilus Karami Y.
21.015 Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin bio metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module Courtade G.
21.005 Crystallization Collective Variable methods Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA Karmakar T.
20.030 Converging experimental and computational views of the knotting mechanism of the smallest knotted protein bio phi-values, transition state, knotted proteins Paissoni C.
20.020 Parallel Bias Metadynamics methods pbmetad, trp-cage, folding Bonomi M.
20.010 Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations materials water, ice, TIP4P, crystallization, EnvironmentSimilarity, RefCV, kernel, VES, variationally enhanced sampling Piaggi P.
20.000 Muscarinic M2 receptor-ligand funnel metadynamics bio multiple walker metadynamics, well-tempered metadynamics, funnel metadynamics, MC-HLDA, GPCR, receptor, Adiabatic Bias MD Capelli R.
19.074 Asymmetric base pair opening in nucleic acids bio double helix, DNA, RNA, unwindability Bussi G.
19.064 Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations materials metadynamics, peptide-surface binding Pfaendtner J.
19.054 MetaFEP methods metadynamics, chemistry, free energy perturbation Piccini G.
19.044 Multithermal-multibaric simulations using VES methods ves, Wang Landau, multicanonical, water, density anomaly Piaggi P.
19.024 PT-MetaD-WTE methods metadynamics, WTE, trp cage, PT Pfaendtner J.
19.014 MIL101(Cr) SBUs assembly materials MOFs, nucleation, self-assembly, metadynamics Salvalaglio M.
19.004 MI Ubiquitin bio metainference, NMR Bonomi M.
23.036 Is the local ion density sufficient to drive NaCl nucleation in vacuum and in water? bio NaCl, nucleation, metadynamics Wang R.
23.026 Machine Learning Nucleation Collective Variables with Graph Neural Networks chemistry Nucleation, Machine Learning, Enhanced Sampling, Collective Variables, Graph Neural Networks Dietrich F.
23.016 Activation/deactivation free-energy profiles for the β2-adrenergic receptor: Ligand modes of action bio G protein coupled receptor, beta-adrenergic, receptor activation, partial agonism, metadynamics Clark T.
23.006 Transcription factor unbinding bio metadynamics, DNA, conformational changes Lüking M.
22.042 Metadynamics of NSP10 and variants bio metadynamics, NSP10, crystal structure, variants Haider S.
22.032 Reciprocal barrier restraint. Application to path-meta-eABF methods restraint, upper wall, lower wall, path colvar, meta-eABF, metadynamics, DRR, protein conformational transition, PROTAC Kolossvary I.
22.022 Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir bio RMSD, protein-ligand interactions Grothaus I.
22.012 Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT bio contact maps, protein-protein interactions Grothaus I.
21.044 NaCl nucleation chemistry metadynamics, DFS clustering Finney A.
21.034 Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics bio reinforced dynamics, bias-exchange metadynamics, parallel-bias metadynamics Wang D.
21.024 Property map collective variable as a useful tool for force field correction chemistry molecular mechanics Spiwok V.
21.014 how to determine statistically accurate conformational ensembles bio metadynamics, metainference, errors, cv, SAXS, ensemble determination Paissoni C.
21.004 Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy bio machine learning, well-tempered metadynamics, path collective variable, potential of mean force, standard binding free energy calculations, host-guest, protein-ligand unbinding Gobbo D.
20.029 High Conformational Flexibility of the E2F1/DP1/DNA complex bio SAXS, protein-DNA complex, hySAXS, ensemble determination Paissoni C.
20.019 Systematic finite-temperature reduction of crystal energy landscapes materials crystals, organics, structure prediction Salvalaglio M.
20.009 The dynamics of linear polyubiquitin bio saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics Camilloni C.
19.083 Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis chemistry metadynamics, chemical reactions, reaction discovery Rizzi V.
19.073 On the role of enthalpic and entropic contributions on the conformational free energy landscape of MIL-101(Cr) building units materials metadynamics, MOF, MIL101Cr, conformational Salvalaglio M.
19.063 Protein-ligand binding through metadynamics with path CVs bio metadynamics, path CVs, ligand binding Bernetti M.
19.053 Capillary fluctuations with PLUMED methods nucleation, surface tension, capillary fluctuations Tribello G.
19.043 Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) methods metadynamics, chemistry, HLDA Piccini G.
19.023 RECT methods metadynamics, replica exchange Bussi G.
19.013 RNA FF FITTING methods force field, RNA Bussi G.
19.003 EMMI ClpP bio metainference, cryo-EM Bonomi M.
23.035 An Extended Metadynamics Protocol for Binding/Unbinding of Peptide Ligands to Class A G-Protein Coupled Receptors bio G protein coupled receptor, peptide ligands, metadynamics, multiple-walker Clark T.
23.025 Probing ion binding to G-quadruplexes and related events chemistry metadynamics, repulsive potential, nucleic acids, G-quadruplexes Poleto M.
23.015 MPCs aggregation bio opes_explore, dimerization, MPCs, self-assembly Tiwari V.
23.005 A general metadynamics protocol to simulate activation/deactivation of Class A GPCRs bio metadynamics, activation/deactivation, activation index, GPCRs, 5HT1A Clark T.
22.041 Skipping the Replica Exchange Ladder with Normalizing Flows methods OPES, alanine, normalizing flows, replica exchange Invernizzi M.
22.031 Rare Event Kinetics from Adaptive Bias Enhanced Sampling methods OPES Flooding, Kinetics, Rate, OPES, Machine Learning Ray D.
22.021 Phase diagram of the TIP4P/Ice water model by enhanced sampling simulations chemistry Ice, water, nucleation, environment similarity, interfaces, phase diagram, multiumbrella Bore S.
22.011 Accelerating all-atom simulations and gaining mechanistic understanding of biophysical systems through State Predictive Information Bottleneck methods metadynamics, membrane permeation, protein folding Mehdi S.
22.000 Amyloid precursor protein processing by human γ-secretase bio Bias Exchange Metadynamics, Helix unfolding, coupled binding Lu X.
21.043 Predicting the Conformational Variability of Oncogenic GTP-bound G12D Mutated KRas-4B Proteins at Cell Membranes chemistry well-tempered metadynamics, KRas-4B, anionic membrane, conformational variability Lu H.
21.033 Multiple-path-metadynamics applied to DNA base-pairing transitions bio path-CV, metadynamics, multiple-walker, dna Pérez-de-Alba-Ortíz A.
21.023 Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling methods enhanced sampling, collective variables, machine learning Rydzewski J.
21.013 Role of vibrational excitation in heterogeneous catalysis chemistry catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption Bal K.
21.003 aSYN SAXS metainference bio metainference, SAXS Lindorff-Larsen K.
20.028 Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane bio metadynamics, KRas-4B, anionic membrane Lu H.
20.018 Free energy barriers from biased molecular dynamics simulations methods kinetics, free energy barriers, chemical reactions, nucleation, metadynamics Bal K.
20.008 Simulating solvation and acidity in complex mixtures with first-principles accuracy. The case of CH3SO3H and H2O2 in phenol chemistry proton trasfer, metadynamics Rossi K.
19.082 Ammonia Borane Dehydrogenation chemistry metadynamics, reaction discovery, hydrogen production, chemistry Rizzi V.
19.072 SINE hairpin MD+NMR bio metadynamics, RNA, NMR Bussi G.
19.062 Elucidating molecular design principles for charge-alternating peptides bio peptide folding, metadynamics, well-tempered ensemble, parallel tempering Pfaendtner J.
19.052 Gibbs free energy of homogeneous nucleation materials nucleation, surface excess free energy Tribello G.
19.042 Harmonic Linear Discriminant Analysis (HLDA) methods metadynamics, chemistry, HLDA Piccini G.
19.032 Chemical reaction in solution using path collective variables based on coordination patterns chemistry chemical reactions, solutions, metadynamics, coordination patterns Pietrucci F.
19.022 eABF simulation of NANMA (alanine dipeptide) methods eABF, DRR, alanine dipeptide Chen H.
19.012 Martini-Beads multi-scale SAXS methods metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex Camilloni C.
19.002 EMMI STRA6 bio metainference, cryo-EM Bonomi M.