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 |
---|---|---|---|---|
22.029 | Angiotensin-1-7_Metadynamics | bio | Metadynamics, Angiotensin-(1-7), peptide | Chi L. |
22.028 | N-glycan conformer distributions in atomistic simulation | bio | REST2, RECT, N-glycan, pucker | Grothaus I. |
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. |
22.026 | Designing Sequence-Defined Peptoids for Fibrillar Self-Assembly and Silicification | materials | Peptoid, silica | Pfaendtner J. |
22.025 | Bubble nucleation rate predictions in a Lennard-Jones fluid | bio | free energies, kinetics, reweighted Jarzynski sampling, neural network, nucleation | Bal K. |
22.024 | Conformational Entropy as a Potential Liability of Computationally Designed Antibodies | bio | metadynamics, conformational entropy, antibody, nanobody | Löhr T. |
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. |
22.022 | Modulation of Multidrug Resistance Protein 1 - mediated transport processes by the antiretroviral drug ritonavir | bio | RMSD, protein-ligand interactions | Grothaus I. |
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. |
22.020 | 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. |
22.019 | Exploring aspartic protease inhibitor binding to design selective antimalarials | bio | ligand binding, loop opening, path CV, funnel metadynamics, drug development | Bobrovs R. |
22.018 | Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations | bio | ligand binding, docking, EMMI, LAT1 | 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. |
22.016 | 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. |
22.015 | Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome | bio | photodynamics, bacteriophytochrome, variationally enhanced sampling | Rydzewski J. |
22.014 | Quasi Liquid Layer Order Parameters | materials | Quasi-Liquid Layer, Steinhardt Order Parameter, Entropy Fingerprint | Shi J. |
22.013 | Ligand dissociation from PreQ1 riboswitch | bio | ligand, RNA, metadynamics, pRAVE | Wang Y. |
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. |
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. |
22.009 | Glycosylation in calixarenes capsule | chemistry | Metadynamics, glycosylation, supramolecular catalysis | Piccini G. |
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. |
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. |
22.006 | Peptide framework for screening the effects of amino acids on assembly | bio | metadynamics, peptides | White A. |
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. |
22.004 | Discover, Sample and Refine. Exploring Chemistry with Enhanced Sampling Techniques | chemistry | reaction discovery, OPES, collective variables | Raucci U. |
22.003 | Exploration vs Convergence Speed in Adaptive-bias Enhanced Sampling | methods | opes, metadynamics, reweighting, alanine, muller | Invernizzi M. |
22.002 | GAMBES_SAMPL5_RATES | other | GAMBES, SAMPL5, Rates, Dynamics, Mechanism, Unbinding | Debnath J. |
22.001 | Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials | methods | enhanced sampling, variationally enhanced sampling, ves, metadynamics, bias representation, wavelets, adam | Pampel B. |
22.000 | Amyloid precursor protein processing by human γ-secretase | bio | Bias Exchange Metadynamics, Helix unfolding, coupled binding | Lu X. |
21.052 | On the Role of Solvent in the Formation of Vacancies on Ibuprofen Crystal Facets | materials | Ibuprofen, unbinding, WTmetaD | Salvalaglio M. |
21.051 | Automatic learning of hydrogen-bond fixes in an AMBER RNA force field | methods | force field, RNA | Bussi G. |
21.050 | N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity | methods | bio | Grothaus I. |
21.049 | Multiple-path-metadynamics and PathMaps | methods | path-CV, metadynamics, multiple-walker, multiple paths, pathmap | Pérez-de-Alba-Ortíz A. |
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. |
21.047 | Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations | materials | pair entropy, metadynamics, ves, solids, crystallization | Piaggi P. |
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. |
21.045 | 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. |
21.044 | NaCl nucleation | chemistry | metadynamics, DFS clustering | Finney A. |
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. |
21.042 | Peptoid-mediated Au nanocrystal growth | materials | parallel-bias metadynamics, peptoid, Au | Qi X. |
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. |
21.040 | 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. |
21.039 | Deep learning the slow modes for rare events sampling | methods | collective variables, machine learning, slow modes, deep-tica, opes | Bonati L. |
21.038 | Towards automated sampling of polymorph nucleation and free energies with SGOOP and metadynamics | materials | metadynamics, SGOOP, nucleation, urea | Zou Z. |
21.037 | Molecular Dynamics simulations of RBD/hACE2 complexes | bio | SARS-CoV-2, COVID-19, MD, human-ACE2, spike, receptor-binding domain | Bonomi M. |
21.036 | 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. |
21.035 | CmuMD simulations of NaCl(aq) at NaCl | chemistry | CmuMD, interface | 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. |
21.033 | Multiple-path-metadynamics applied to DNA base-pairing transitions | bio | path-CV, metadynamics, multiple-walker, dna | Pérez-de-Alba-Ortíz A. |
21.032 | Metal-coupled folding mechanism to metallothionein | bio | parallel bias metadynamics, well tempered metadynamics, metal binding, metalloprotein, zinc coordination | Diaz M. |
21.031 | Photo-switchable sulfonulureas in KATP channel | bio | metadynamics, photo-pharmacology, sulfonylureas potasium ion-channels | Walczewska-Szewc K. |
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. |
21.029 | Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs | bio | metadynamics, small peptide, machine learning | Tiwary P. |
21.028 | From Enhanced Sampling to Reaction Profiles | methods | collective variables, multi-state, machine learning, Deep-TDA | Trizio E. |
21.027 | EGFR activating mutations mechanism | bio | metadynamics, well-tempered ensemble, Parallel-tempering, EGFR, L858R, A763-Y764insFQEA, D770-N771insNPG, Delta-ELREA | Gervasio F. |
21.026 | Probing allosteric regulations with coevolution-driven molecular simulations | bio | metadynamics, coevolution, allostery, adenylate cyclase | Colizzi F. |
21.025 | Computational and biochemical analysis of type IV pilus dynamics and stability | bio | molecular dynamics, calcium binding, Type IV pilus | Karami Y. |
21.024 | Property map collective variable as a useful tool for force field correction | chemistry | molecular mechanics | Spiwok V. |
21.023 | Multiscale Reweighted Stochastic Embedding (MRSE) - Deep Learning of Collective Variables for Enhanced Sampling | methods | enhanced sampling, collective variables, machine learning | Rydzewski J. |
21.022 | Predictive theoretical framework for dynamic control of bio-inspired hybrid nanoparticle self-assembly | materials | parallel bias metadynamics, adsorption, peptide | Qi X. |
21.021 | ATLAS | methods | Machine Learning, Metadynamics | Giberti F. |
21.020 | Reweighted Jarzynski sampling | methods | free energies, steered MD, neural network, nonequilibrium work, nucleation, chemical reactions | Bal K. |
21.019 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | materials | Crystal/Energy landscapes, Molecular Dynamics, Ibuprofen | Salvalaglio M. |
21.018 | Localized Volume-based Metadynamics | bio | LV-MetaD, Volume-based MetaD, Metadynamics, Ligand binding, Induced-fit effects, Binding pose identification | Capelli R. |
21.017 | All-atom simulations of the Vav1 AD construct | bio | metadynamics, parallel-bias, well-tempered | Orioli S. |
21.016 | MD SAXS GTPase associated center | bio | metadynamics, RNA, folding, SAXS | Bussi G. |
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. |
21.014 | how to determine statistically accurate conformational ensembles | bio | metadynamics, metainference, errors, cv, SAXS, ensemble determination | Paissoni C. |
21.013 | Role of vibrational excitation in heterogeneous catalysis | chemistry | catalysis, vibrational excitation, free energy barriers, dissociation, chemisorption | Bal K. |
21.012 | NMR-Guided Rational Engineering of Endocellulase from Acidothermus Cellulolyticus for Reducing Product Inhibition | bio | funnel metadynamics | Pfaendtner J. |
21.011 | CmuMD simulations of NaCl(aq) at graphite | chemistry | CmuMD, DFS clustering | Finney A. |
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. |
21.009 | Nucleation rates from small scale atomistic simulations and transition state theory | materials | kinetics, free energy barriers, nucleation, droplets, metadynamics | Bal K. |
21.008 | Multi-replica biased sampling for photoisomerization processes in conjugated polymers | methods | metadynamics, FEP, replica-exchange | Pietropaolo A. |
21.007 | Sampling enhancement by metadynamics driven by machine learning and de novo protein modelling | bio | metadynamics, machine learning, protein folding | Spiwok V. |
21.006 | OPES, On-the-fly Probability Enhanced Sampling Method | methods | opes, alanine dipeptide, well-tempered, multithermal, multiumbrella | Invernizzi M. |
21.005 | Crystallization Collective Variable | methods | Crystallization, Collective Variable, OPES, Structure Factor, Phase transitions, Deep-LDA | Karmakar T. |
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. |
21.003 | aSYN SAXS metainference | bio | metainference, SAXS | Lindorff-Larsen K. |
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. |
21.001 | Substrate recognition and catalysis by glycosaminoglycan sulfotransferases | bio | metadynamics, well-tempered metadynamics, puckering, coordination | Ferreira 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. |
20.034 | 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. |
20.033 | COVID-19 Spike protein opening transition mechanism | bio | EMMI, CryoEM, COVID-19, Spike, Metainference | Brotzakis F. |
20.032 | Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil | materials | clustering, conformational isomers | Salvalaglio M. |
20.031 | Soft fluorescent nanoshuttles targeting receptors | chemistry | polymers, receptors, nanoparticles, fluorescent probes | Pietropaolo A. |
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. |
20.029 | High Conformational Flexibility of the E2F1/DP1/DNA complex | bio | SAXS, protein-DNA complex, hySAXS, ensemble determination | Paissoni C. |
20.028 | Well-tempered metadynamics on wt/onc KRas-4B, binding on the anionic membrane | bio | metadynamics, KRas-4B, anionic membrane | Lu H. |
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. |
20.026 | Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor | bio | Metadynamics, Umbrella sampling | Peters B. |
20.025 | The role of water in host-guest interaction | bio | ligand binding, water, opes, SAMPL5 | Rizzi V. |
20.024 | Gaussian Mixture Based Enhanced Sampling (GAMBES) | methods | enhanced sampling, probability based sampling, chemical reactions, rate calculation, static bias | Debnath J. |
20.023 | metadynminer and metadynminer3d | methods | metadynamics, visualization, R | Spiwok V. |
20.022 | Unified Approach to Enhanced Sampling | methods | OPES, expanded ensembles, importance sampling | Invernizzi M. |
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. |
20.020 | Parallel Bias Metadynamics | methods | pbmetad, trp-cage, folding | Bonomi M. |
20.019 | Systematic finite-temperature reduction of crystal energy landscapes | materials | crystals, organics, structure prediction | Salvalaglio M. |
20.018 | Free energy barriers from biased molecular dynamics simulations | methods | kinetics, free energy barriers, chemical reactions, nucleation, metadynamics | Bal K. |
20.017 | FISST | methods | FISST, force, peptide, sampling, tempering | Hocky G. |
20.016 | Predicting polymorphism in molecular crystals using orientational entropy | materials | metadynamics, polymorphism, urea, naphthalene, g(r), pair correlation, entropy | Piaggi P. |
20.015 | Rational design of ASCT2 inhibitors using an integrated experimental-computational approach | bio | ASCT2 transporter, small-molecules, cryo-EM, metainference | Bonomi M. |
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. |
20.013 | Improving accuracy of biased Alchemistic simulations | methods | flying Gaussian method, Alchemistic simulations, thermodynamic integration, reweighting | Spiwok V. |
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. |
20.011 | Uremic toxin analysis | bio | metadynamics, uremic toxin, serum albumin | Pfaendtner J. |
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. |
20.009 | The dynamics of linear polyubiquitin | bio | saxs, martini, metainference, metadynamics, ubiquitin, protein dynamics | Camilloni C. |
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. |
20.007 | Discovering loop conformational flexibility in T4lysozyme mutants through artificial intelligence aided molecular dynamics | bio | metadynamics, loop movement, artificial intelligence | Tiwary P. |
20.006 | Class B GPCR activation mechanism | bio | metadynamics, well-tempered ensemble, multiple walkers, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. |
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. |
20.004 | Data-driven collective variables for enhanced sampling | methods | collective variables, machine learning, deep-lda | Bonati L. |
20.003 | Enhanced sampling of transition states | methods | Variationally Enhanced Sampling, Target distribution, Transition state, Enhanced Sampling, Nucleation, chemical reaction | Debnath J. |
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. |
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. |
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. |
19.083 | Blind Search for Complex Chemical Pathways Using Harmonic Linear Discriminant Analysis | chemistry | metadynamics, chemical reactions, reaction discovery | Rizzi V. |
19.082 | Ammonia Borane Dehydrogenation | chemistry | metadynamics, reaction discovery, hydrogen production, chemistry | Rizzi V. |
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. |
19.080 | Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium | methods | ves, variationally enhanced sampling, vibrational excitation, chemical reactions | Bal K. |
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. |
19.078 | Iterative unbiasing of quasi-equilibrium sampling | methods | metadynamics, reweighting | Giberti F. |
19.077 | Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. |
19.076 | Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones | bio | molecular chaperones, Hsp70, protein folding, non equilibrium thermodynamics | Assenza S. |
19.075 | PYCV - a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python | other | Python, automatic differentiation | Giorgino T. |
19.074 | Asymmetric base pair opening in nucleic acids | bio | double helix, DNA, RNA, unwindability | Bussi G. |
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. |
19.072 | SINE hairpin MD+NMR | bio | metadynamics, RNA, NMR | Bussi G. |
19.071 | Time-independent free energies from metadynamics via Mean Force Integration | methods | metadynamics, mean force integration, MFI, thermodynamic integration | Salvalaglio M. |
19.070 | Unexpected Dynamics in the UUCG RNA Tetraloop | bio | well-tempered metadynamics, RNA, UUCG, maximum entropy | Bottaro S. |
19.069 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | materials | ibuprofen, crystal, solvent, surface | Salvalaglio M. |
19.068 | Rethinking Metadynamics | methods | metadynamics, opes, convergence | Invernizzi M. |
19.067 | Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways | bio | metadynamics, ligand unbinding | Rydzewski J. |
19.066 | Finding ligand unbinding reaction pathways | methods | maze, ligand unbinding | Rydzewski J. |
19.065 | Molecular Enhanced Sampling with Autoencoders | methods | enhanced sampling, collective variables, deep learning | Chen W. |
19.064 | Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations | materials | metadynamics, peptide-surface binding | Pfaendtner J. |
19.063 | Protein-ligand binding through metadynamics with path CVs | bio | metadynamics, path CVs, ligand binding | Bernetti M. |
19.062 | Elucidating molecular design principles for charge-alternating peptides | bio | peptide folding, metadynamics, well-tempered ensemble, parallel tempering | Pfaendtner J. |
19.061 | Diffusion in porous materials | materials | metadynamics, porous materials, diffusion | Jelfs K. |
19.060 | Neural networks-based variationally enhanced sampling | methods | ves, neural networks | Bonati L. |
19.059 | cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide | bio | bias-exchange metadynamics, cis-trans isomerization | Marinelli F. |
19.058 | Constrained MD for maintaining a cavity in a calculation | chemistry | constrained MD, porous molecules, porosity, cavity | Jelfs K. |
19.057 | SAXS ensembles using Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, ensemble determination, metadynamics, protein dynamics | Paissoni C. |
19.056 | maze | methods | maze, ligand unbinding | Rydzewski J. |
19.055 | Flying Gaussian method | methods | flying Gaussians, alanine dipeptide, peptide bond, Met-enkephalin | Spiwok V. |
19.054 | MetaFEP | methods | metadynamics, chemistry, free energy perturbation | Piccini G. |
19.053 | Capillary fluctuations with PLUMED | methods | nucleation, surface tension, capillary fluctuations | Tribello G. |
19.052 | Gibbs free energy of homogeneous nucleation | materials | nucleation, surface excess free energy | Tribello G. |
19.051 | Solid liquid interfacial free energy out of equilibrium | materials | metadynamics, nucleation, surface excess free energy | Tribello G. |
19.050 | Using intrinsic surface to calculate the free energy change when nanoparticles adsorb on membranes | chemistry | metadynamics, membranes, Willard Chandler surface | Tribello G. |
19.049 | Determining the sizes of solid/liquid clusters in MD trajectories of nucleation | methods | nucleation, metadynamics, clustering, Steinhardt order parameters | Tribello G. |
19.048 | Understanding Ligand Binding Selectivity in a Prototypical GPCR Family | bio | metadynamics, Parallel-tempering metadynamics, GPCRs, ligand binding | Gervasio F. |
19.047 | Close Structure | methods | metadynamics, RMSD, path collective variables, property map | Spiwok V. |
19.046 | Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding | bio | VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation | Brotzakis F. |
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. |
19.044 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, water, density anomaly | Piaggi P. |
19.043 | Multi Class - Harmonic Linear Discriminant Analysis (MC-HLDA) | methods | metadynamics, chemistry, HLDA | Piccini G. |
19.042 | Harmonic Linear Discriminant Analysis (HLDA) | methods | metadynamics, chemistry, HLDA | Piccini 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. |
19.040 | Optimal Metric for Path Collective Variables | bio | metadynamics, path collective variables, sgoop, alanine tripeptide, conformational changes, optimal path | Gervasio F. |
19.039 | Funnel Metadynamics | bio | funnel-metadynamics, absolute binding free energy, ligand-receptor complexes | Limongelli V. |
19.038 | native state dynamics of human and mouse b2m | bio | metainference, NMR, chemical shifts, metadynamics, protein dynamics, aggregation | Camilloni C. |
19.037 | Scission free energy of organic dyes | chemistry | metadynamics, multiple walkers, matheval/lepton | Raiteri P. |
19.036 | Thermodynamics and kinetics of G protein-coupled receptor activation | bio | metadynamics, allostery, receptor conformation, GPCR, pharmacology | Provasi D. |
19.035 | Dimerization of GPCRs from coarse-grained umbrella sampling | bio | Umbrella sampling, coarse-grained, GPCR, protein-protein binding free energy, dimerization | Provasi D. |
19.032 | Chemical reaction in solution using path collective variables based on coordination patterns | chemistry | chemical reactions, solutions, metadynamics, coordination patterns | Pietrucci F. |
19.031 | Ice nucleation using PIV-based path coordinates | materials | phase transitions, nucleation, TIP4P, path CV, PIV, metadynamics | Pipolo S. |
19.029 | WTE-metaD of FF domain of URNF1 C57D variant | bio | metadynamics, mutations, post-translational modification, ff domain | Papaleo E. |
19.028 | pRAVE | methods | RAVE, reaction coordinate, deep learning, metadynamics, kinetics | Tiwary P. |
19.027 | Multithermal-multibaric simulations using VES | methods | ves, Wang Landau, multicanonical, liquid sodium, density anomaly | Piaggi P. |
19.026 | Ice Nucleation on Cholesterol Crystals | materials | forward flux sampling, crystal nucleation, water, ice, organic crystals | Sosso G. |
19.025 | Metadynamic metainference Convergence towards force field independent structural ensembles of a disordered peptide | bio | metainference, NMR, protein dynamics, force-fields | Camilloni C. |
19.024 | PT-MetaD-WTE | methods | metadynamics, WTE, trp cage, PT | Pfaendtner J. |
19.023 | RECT | methods | metadynamics, replica exchange | Bussi G. |
19.022 | eABF simulation of NANMA (alanine dipeptide) | methods | eABF, DRR, alanine dipeptide | Chen H. |
19.021 | Coarse-Grained Directed Simulation | methods | experiment directed simulation, coarse-grain, bias | Hocky G. |
19.020 | PTMetaD-WTE simulation of the Ntail IDP | bio | metadynamics, IDPs, protein folding | Bernetti M. |
19.019 | FA-MetaD-JCP-Wang-et-al | bio | Frequency adaptive metadynamics; peptide | Lindorff-Larsen K. |
19.018 | Excited state FEP/Metadynamics simulations | chemistry | metadynamics, FEP, excited states, conjugated polymers, torsional potential | Pietropaolo A. |
19.017 | Ligand binding pathways exploration | bio | metadynamics, ligand binding | Capelli R. |
19.016 | Succinnic acid gamma polymorph | materials | Succinnic acid, conformers, polymorphs, metadynamics | Salvalaglio M. |
19.015 | Ibuprofen conformational dynamics and thermodynamics surface | materials | Ibuprofen, crystal, surface, solvents, conformers, metadynamics | Salvalaglio M. |
19.014 | MIL101(Cr) SBUs assembly | materials | MOFs, nucleation, self-assembly, metadynamics | Salvalaglio M. |
19.013 | RNA FF FITTING | methods | force field, RNA | Bussi G. |
19.012 | Martini-Beads multi-scale SAXS | methods | metainference, SAXS, martini, structure refinement, nucleic-acids, protein complex | Camilloni C. |
19.011 | Automatic Gradient Computation for Collective Variables | other | gradient, differentiation, curvature | Giorgino T. |
19.010 | Multi-domain protein dynamics | bio | metainference, NMR, protein dynamics | Camilloni C. |
19.009 | RNA tetraloops folding | bio | metadynamics, RNA, folding | Bussi G. |
19.008 | anncolvar | methods | neural network, dimensionality reduction | Spiwok V. |
19.007 | EMMI Microtubules | bio | metainference, cryo-EM | Bonomi M. |
19.006 | Flying Gaussian proof | methods | flying Gaussians, alanine dipeptide | Spiwok V. |
19.005 | Cmyc small molecule interaction | bio | metadynamics, metainference, disordered protein, small molecule interaction, c-myc, cancer, IDP | Heller G. |
19.004 | MI Ubiquitin | bio | metainference, NMR | Bonomi M. |
19.003 | EMMI ClpP | bio | metainference, cryo-EM | Bonomi M. |
19.002 | EMMI STRA6 | bio | metainference, cryo-EM | Bonomi M. |
19.001 | RNA SHAPE | bio | metadynamics, RNA, ligand binding | Bussi G. |
19.000 | VesDeltaF | methods | VES, convergence, suboptimal CVs | Invernizzi M. |