| scholarly article | Q13442814 |
| P2093 | author name string | W G Noid | |
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| Predicting the thermodynamics by using state-dependent interactions | Q46791657 | ||
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| Automatic prediction of protein interactions with large scale motion | Q47597143 | ||
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| An iterative method for extracting energy-like quantities from protein structures. | Q37262313 | ||
| Force field bias in protein folding simulations | Q37263580 | ||
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| The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures | Q37291590 | ||
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| Insights from coarse-grained Gō models for protein folding and dynamics | Q37462223 | ||
| Three-body interactions improve the prediction of rate and mechanism in protein folding models | Q37589571 | ||
| Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides | Q37603743 | ||
| How optimization of potential functions affects protein folding | Q37611237 | ||
| Basic ingredients of free energy calculations: a review | Q37662435 | ||
| Multiscale simulation of soft matter systems | Q37693124 | ||
| Global dynamics of proteins: bridging between structure and function | Q37700683 | ||
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| Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. | Q37782011 | ||
| Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems | Q37804856 | ||
| Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. | Q33432712 | ||
| Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis | Q33568300 | ||
| Polarizable water model for the coarse-grained MARTINI force field | Q33604854 | ||
| Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology | Q33619016 | ||
| Multiscale coarse-graining of the protein energy landscape | Q33619186 | ||
| Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models | Q33632680 | ||
| Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data | Q33636214 | ||
| PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy | Q33653515 | ||
| CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. | Q33693774 | ||
| Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins | Q33718901 | ||
| Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. | Q33733600 | ||
| Go-ing for the prediction of protein folding mechanisms | Q33750611 | ||
| Mechanical unfolding of RNA hairpins | Q33784317 | ||
| A coarse-grained model for amorphous and crystalline fatty acids | Q33808172 | ||
| On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties | Q33835224 | ||
| Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes | Q33900447 | ||
| Anisotropy of fluctuation dynamics of proteins with an elastic network model | Q33931550 | ||
| Molecular crowding enhances native state stability and refolding rates of globular proteins | Q33935100 | ||
| MAVENs: motion analysis and visualization of elastic networks and structural ensembles | Q33944857 | ||
| Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis | Q33947913 | ||
| SMOG@ctbp: simplified deployment of structure-based models in GROMACS | Q33957517 | ||
| Flexibility and packing in proteins | Q34008934 | ||
| A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field | Q34011687 | ||
| Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures. | Q34019396 | ||
| A structure-based method for derivation of all-atom potentials for protein folding | Q34024626 | ||
| Simulations of beta-hairpin folding confined to spherical pores using distributed computing | Q34030924 | ||
| The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation | Q34037348 | ||
| Experimental evaluation of topological parameters determining protein-folding rates | Q34074395 | ||
| A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations | Q34085742 | ||
| Computer simulation of protein folding | Q34099184 | ||
| Keeping it in the family: folding studies of related proteins | Q34141529 | ||
| Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA. | Q34144275 | ||
| Extending the PRIME model for protein aggregation to all 20 amino acids | Q34156490 | ||
| Simple simulations of DNA condensation | Q34174716 | ||
| Dynamics of proteins in crystals: comparison of experiment with simple models | Q34178430 | ||
| Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model | Q34188438 | ||
| Polarizable force fields | Q34215898 | ||
| Structural transformation in supercooled water controls the crystallization rate of ice. | Q34235591 | ||
| Protein folding theory: from lattice to all-atom models | Q34243263 | ||
| High-resolution protein folding with a transferable potential | Q34244862 | ||
| A structurally relevant coarse-grained model for cholesterol | Q34250580 | ||
| Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements | Q34285601 | ||
| Coarse-Grained Molecular Models of Water: A Review | Q34294897 | ||
| Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics | Q34300133 | ||
| Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B. | Q34341336 | ||
| Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. | Q34350367 | ||
| The role of shape in determining molecular motions | Q34351341 | ||
| Coarse-grained modeling of the actin filament derived from atomistic-scale simulations | Q34354242 | ||
| Spin glasses and the statistical mechanics of protein folding | Q34358450 | ||
| Recovering physical potentials from a model protein databank | Q34358926 | ||
| An empirical energy function for threading protein sequence through the folding motif | Q34365419 | ||
| Chemically accurate coarse graining of double-stranded DNA. | Q34377420 | ||
| Interfaces and the driving force of hydrophobic assembly | Q34455286 | ||
| Contact order, transition state placement and the refolding rates of single domain proteins. | Q34464266 | ||
| A coarse-grained model of DNA with explicit solvation by water and ions | Q34481643 | ||
| Dynamic pathways for viral capsid assembly | Q34680422 | ||
| Modeling the lipid component of membranes | Q34774296 | ||
| Relation between native ensembles and experimental structures of proteins | Q34984169 | ||
| Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back | Q35000496 | ||
| A natural coarse graining for simulating large biomolecular motion | Q35012272 | ||
| Optimal prediction and the Mori-Zwanzig representation of irreversible processes | Q35101724 | ||
| Minimalist models for protein folding and design | Q35119722 | ||
| Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy | Q35234492 | ||
| Three-helix-bundle protein in a Ramachandran model | Q35569643 | ||
| Protein topology determines binding mechanism | Q35734060 | ||
| Development of novel statistical potentials for protein fold recognition | Q35749519 | ||
| How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta | Q35752174 | ||
| Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution | Q35808767 | ||
| Coarse-grained peptide modeling using a systematic multiscale approach | Q35812310 | ||
| Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data | Q35855047 | ||
| Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born | Q35948015 | ||
| A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO). | Q35962923 | ||
| Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. | Q35972950 | ||
| Coarse-grained sequences for protein folding and design | Q35977668 | ||
| Coarse-grained models for proteins | Q36101080 | ||
| Modeling water, the hydrophobic effect, and ion solvation | Q36115443 | ||
| Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. | Q36129144 | ||
| How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations | Q36160854 | ||
| Mesoscopic modeling for nucleic acid chain dynamics. | Q36248801 | ||
| Implicit solvent simulation models for biomembranes | Q36269271 | ||
| Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets | Q36278905 | ||
| Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes | Q36281424 | ||
| OPUS-Ca: a knowledge-based potential function requiring only Calpha positions | Q36393213 | ||
| Systematic multiscale simulation of membrane protein systems | Q36410326 | ||
| Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. | Q36475375 | ||
| Development of a physics-based force field for the scoring and refinement of protein models | Q36510582 | ||
| Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles | Q36546184 | ||
| Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding | Q36590747 | ||
| Reduced atomic pair-interaction design (RAPID) model for simulations of proteins. | Q36631234 | ||
| Boltzmann-type distribution of side-chain conformation in proteins | Q36631481 | ||
| Recent advances in implicit solvent-based methods for biomolecular simulations | Q36662616 | ||
| Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms | Q36666278 | ||
| Multiscale modeling of biomolecular systems: in serial and in parallel | Q36769218 | ||
| Computational techniques for efficient conformational sampling of proteins | Q36769352 | ||
| On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review | Q36849786 | ||
| Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? | Q36850366 | ||
| OPUS-Rota: a fast and accurate method for side-chain modeling | Q36851694 | ||
| Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model | Q36869889 | ||
| A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography | Q36926799 | ||
| Systematic multiscale parameterization of heterogeneous elastic network models of proteins | Q36938668 | ||
| Biomolecularmodeling and simulation: a field coming of age. | Q37827906 | ||
| Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome | Q37845632 | ||
| Coarse-grained modeling for macromolecular chemistry | Q37848249 | ||
| Coarse-grained models for protein aggregation. | Q37849429 | ||
| Toy amphiphiles on the computer: What can we learn from generic models? | Q37894634 | ||
| Capturing the essence of folding and functions of biomolecules using coarse-grained models | Q37939507 | ||
| Coarse-graining of multiprotein assemblies | Q37978686 | ||
| Coarse-grained molecular simulations of large biomolecules | Q37988161 | ||
| On developing coarse-grained models for biomolecular simulation: a review | Q38017092 | ||
| Systematic methods for structurally consistent coarse-grained models | Q38049271 | ||
| Coarse-graining methods for computational biology | Q38085672 | ||
| Perspective on the Martini model. | Q38109488 | ||
| The origins of asymmetry in the folding transition states of protein L and protein G. | Q38270380 | ||
| Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction | Q38270534 | ||
| Multiscale characterization of protein conformational ensembles | Q38272896 | ||
| A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties | Q38422997 | ||
| Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer | Q38434413 | ||
| Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain | Q38533275 | ||
| Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration | Q38646397 | ||
| Polarizable Force Fields: History, Test Cases, and Prospects | Q38658999 | ||
| Polarization effects in molecular mechanical force fields | Q39600496 | ||
| Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions | Q39632778 | ||
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| Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water | Q40275897 | ||
| Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations | Q40290793 | ||
| Improved Parameters for the Martini Coarse-Grained Protein Force Field. | Q40295743 | ||
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| Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures | Q40775428 | ||
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| Simulating DNA at low resolution | Q41052965 | ||
| Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins | Q41063147 | ||
| Protein function in the crystal | Q41107799 | ||
| Comparison of database potentials and molecular mechanics force fields | Q41420412 | ||
| vGNM: a better model for understanding the dynamics of proteins in crystals | Q41434271 | ||
| Computational approaches to modeling viral structure and assembly | Q41616699 | ||
| Coarse-grained model for simulation of RNA three-dimensional structures. | Q41688309 | ||
| Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins | Q41734718 | ||
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| A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. | Q42084202 | ||
| Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations | Q42100732 | ||
| Fast procedure for reconstruction of full-atom protein models from reduced representations. | Q30367164 | ||
| Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints | Q30369481 | ||
| Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane. | Q30370775 | ||
| Polymer principles in protein structure and stability. | Q30371172 | ||
| A computer model to dynamically simulate protein folding: studies with crambin. | Q30377365 | ||
| Restriction versus guidance in protein structure prediction. | Q30380107 | ||
| Martini Coarse-Grained Force Field: Extension to Carbohydrates. | Q30381806 | ||
| Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions. | Q30384466 | ||
| A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. | Q30385731 | ||
| On the formation of protein tertiary structure on a computer | Q30389569 | ||
| Trends in template/fragment-free protein structure prediction | Q30400985 | ||
| Coarse-grained force field: general folding theory | Q30403444 | ||
| CASP9 assessment of free modeling target predictions | Q30408132 | ||
| GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction | Q30408272 | ||
| Refinement of protein structure homology models via long, all-atom molecular dynamics simulations | Q30415550 | ||
| AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing | Q30416167 | ||
| Genomics-aided structure prediction | Q30417896 | ||
| The coarse-grained OPEP force field for non-amyloid and amyloid proteins. | Q30418632 | ||
| How to derive a protein folding potential? A new approach to an old problem | Q30426274 | ||
| Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment | Q30427872 | ||
| An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction | Q30429585 | ||
| Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations | Q30477971 | ||
| Dynamics of allosteric transitions in GroEL. | Q30478627 | ||
| Coarse-grained free energy functions for studying protein conformational changes: a double-well network model | Q30480702 | ||
| Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins | Q30482136 | ||
| Four-scale description of membrane sculpting by BAR domains | Q30483300 | ||
| Application of elastic network models to proteins in the crystalline state | Q30483908 | ||
| Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations | Q30491561 | ||
| Current status of the AMOEBA polarizable force field | Q30495924 | ||
| Protein-DNA docking with a coarse-grained force field | Q30529906 | ||
| Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data | Q31135862 | ||
| Iterative predictor-corrector method for extraction of the pair interaction from structural data for dense classical liquids | Q31930348 | ||
| Single-molecule dynamics reveals cooperative binding-folding in protein recognition | Q33250076 | ||
| Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials. | Q50085819 | ||
| Coarse-grain modelling of DMPC and DOPC lipid bilayers. | Q50113427 | ||
| Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go? | Q50142211 | ||
| Microtubule elasticity: connecting all-atom simulations with continuum mechanics. | Q50196509 | ||
| The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure. | Q50497430 | ||
| Generalized Yvon-Born-Green theory for molecular systems. | Q50557732 | ||
| Mori-Zwanzig formalism as a practical computational tool. | Q50563263 | ||
| Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. | Q50708482 | ||
| Anisotropic network model: systematic evaluation and a new web interface. | Q50713107 | ||
| Optimized interactions for targeted self-assembly: application to a honeycomb lattice. | Q50734134 | ||
| Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. | Q50923993 | ||
| Coarse graining of nonbonded degrees of freedom. | Q50942606 | ||
| A coarse grain model for DNA. | Q51053784 | ||
| Dynamic evolution in coarse-grained molecular dynamics simulations of polyethylene melts. | Q51065072 | ||
| Thermodynamic consistency in variable-level coarse graining of polymeric liquids. | Q51291538 | ||
| Concurrent dual-resolution Monte Carlo simulation of liquid methane. | Q51293710 | ||
| Speed up of dynamic observables in coarse-grained molecular-dynamics simulations of unentangled polymers. | Q51354527 | ||
| Statistical mechanics of coarse graining: estimating dynamical speedups from excess entropies. | Q51392023 | ||
| Obtaining fully dynamic coarse-grained models from MD. | Q51585145 | ||
| Let's get honest about sampling. | Q51604998 | ||
| The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials. | Q51607446 | ||
| Coarse-grained model of nucleic acid bases. | Q51614529 | ||
| DNA nanotweezers studied with a coarse-grained model of DNA. | Q51696669 | ||
| Main phase transition in lipid bilayers: Phase coexistence and line tension in a soft, solvent-free, coarse-grained model. | Q51701792 | ||
| The limited role of nonnative contacts in the folding pathways of a lattice protein. | Q51814887 | ||
| Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl. | Q51832438 | ||
| On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. | Q51848746 | ||
| Large-scale molecular dynamics simulations of self-assembling systems. | Q51871584 | ||
| Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors. | Q51874544 | ||
| Combining a polarizable force-field and a coarse-grained polarizable solvent model: application to long dynamics simulations of bovine pancreatic trypsin inhibitor. | Q51890634 | ||
| Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations. | Q51895864 | ||
| Multiscale coarse-graining of monosaccharides. | Q51906164 | ||
| A coarse-grained protein force field for folding and structure prediction. | Q51911563 | ||
| Protein conformational transitions explored by mixed elastic network models. | Q51911720 | ||
| Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. | Q51916177 | ||
| Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. | Q51918735 | ||
| Modeling real dynamics in the coarse-grained representation of condensed phase systems. | Q51930456 | ||
| Effective potentials for folding proteins. | Q51943990 | ||
| Automatic domain decomposition of proteins by a Gaussian Network Model. | Q51986886 | ||
| Deriving effective mesoscale potentials from atomistic simulations. | Q52010759 | ||
| Predicting novel protein folds by using FRAGFOLD. | Q52046754 | ||
| Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. | Q52053541 | ||
| On the design and analysis of protein folding potentials. | Q52078678 | ||
| Knowledge-based scoring function to predict protein-ligand interactions. | Q52083236 | ||
| Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. | Q52310162 | ||
| Contact potential that recognizes the correct folding of globular proteins | Q52412013 | ||
| Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. | Q52451138 | ||
| Hamiltonian adaptive resolution simulation for molecular liquids. | Q52639398 | ||
| Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide. | Q53027596 | ||
| A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements. | Q53189978 | ||
| Mechanical unfolding of RNA: from hairpins to structures with internal multiloops | Q33259722 | ||
| Binding-induced folding of a natively unstructured transcription factor. | Q33327692 | ||
| Origins of structure in globular proteins | Q33356189 | ||
| Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues | Q33372639 | ||
| Protein-protein docking with a reduced protein model accounting for side-chain flexibility | Q42102959 | ||
| The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models | Q42145221 | ||
| Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin | Q42150750 | ||
| Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides | Q42154900 | ||
| Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. | Q42538747 | ||
| NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis | Q42553727 | ||
| SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. | Q42554402 | ||
| An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability | Q42573100 | ||
| Insights on protein-DNA recognition by coarse grain modelling | Q42631625 | ||
| Physical arguments for distance-weighted interactions in elastic network models for proteins | Q42633166 | ||
| Conformational change of proteins arising from normal mode calculations | Q42646780 | ||
| A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins | Q42662065 | ||
| Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase | Q42666690 | ||
| Selection of optimal variants of Gō-like models of proteins through studies of stretching | Q42771246 | ||
| Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models | Q42915927 | ||
| The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials | Q42938319 | ||
| Multiscale investigation of chemical interference in proteins | Q43066617 | ||
| Systematic coarse-graining of molecular models by the Newton inversion method | Q43161086 | ||
| Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model | Q43229898 | ||
| P433 | issue | 9 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 090901 | |
| P577 | publication date | 2013-09-01 | |
| P1433 | published in | Journal of Chemical Physics | Q900472 |
| P1476 | title | Perspective: Coarse-grained models for biomolecular systems | |
| P478 | volume | 139 |
| Q57434029 | A Discontinuous Potential Model for Protein-Protein Interactions |
| Q57372301 | A Review of Multiscale Computational Methods in Polymeric Materials |
| Q47266641 | A coarse-grained model for DNA origami. |
| Q51038351 | A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect. |
| Q47697536 | A multi-state coarse grained modeling approach for an intrinsically disordered peptide |
| Q50755403 | A new algorithm for construction of coarse-grained sites of large biomolecules. |
| Q46330754 | A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2-microglobulin. |
| Q40152123 | A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide). |
| Q57368936 | Adaptive resolution simulation of polarizable supramolecular coarse-grained water models |
| Q47687957 | Adaptive resolution simulations of biomolecular systems. |
| Q90218745 | Advances in coarse-grained modeling of macromolecular complexes |
| Q57547140 | Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations |
| Q37549101 | All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. |
| Q45972178 | An implicit divalent counterion force field for RNA molecular dynamics. |
| Q51518571 | Assembly of nothing: equilibrium fluids with designed structured porosity. |
| Q60909749 | Bayesian selection for coarse-grained models of liquid water |
| Q53178189 | Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. |
| Q50634792 | Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. |
| Q92955138 | Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio |
| Q50855257 | C-IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids. |
| Q36277923 | CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences |
| Q34503075 | COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids |
| Q102218441 | Coarse graining molecular dynamics with graph neural networks |
| Q96231469 | Coarse-grained (hybrid) integrative modeling of biomolecular interactions |
| Q40152225 | Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles. |
| Q26749123 | Coarse-grained modeling of RNA 3D structure |
| Q44127104 | Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation |
| Q43817739 | Coarse-graining DNA for simulations of DNA nanotechnology. |
| Q83558323 | Coarse-graining auto-encoders for molecular dynamics |
| Q89512342 | Coarse-scale PDEs from fine-scale observations via machine learning |
| Q52588423 | Communication: Adaptive boundaries in multiscale simulations. |
| Q40017907 | Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information |
| Q50975201 | Communication: Pseudoisomorphs in liquids with intramolecular degrees of freedom. |
| Q50786099 | Computation of the memory functions in the generalized Langevin models for collective dynamics of macromolecules. |
| Q64245550 | Computational Modeling of Realistic Cell Membranes |
| Q47121058 | Computer Simulations of Lipid Nanoparticles. |
| Q57372065 | Computer Simulations of Soft Matter: Linking the Scales |
| Q46925379 | Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts |
| Q57547116 | Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations |
| Q51033600 | Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwanzig formulation. |
| Q47209365 | Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion. |
| Q50201288 | Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow. |
| Q54858027 | Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics. |
| Q92943862 | Development of Coarse-Grained Models for Polymers by Trajectory Matching |
| Q44875489 | Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. |
| Q62698602 | Drug-Membrane Permeability across Chemical Space |
| Q41026777 | Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence |
| Q46067457 | Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics |
| Q47591189 | Dynamic principle for ensemble control tools. |
| Q51557920 | Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. |
| Q41127049 | Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. |
| Q48041828 | Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid. |
| Q64101280 | Energy renormalization for coarse-graining polymers having different segmental structures |
| Q57581983 | Energy-Renormalization for Achieving Temperature Transferable Coarse-Graining of Polymer Dynamics |
| Q50656711 | Energy-conserving coarse-graining of complex molecules. |
| Q30367786 | Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange. |
| Q50928163 | Equilibrium cluster fluids: pair interactions via inverse design. |
| Q46464597 | Exact dynamical coarse-graining without time-scale separation |
| Q48061878 | Exploring biomolecular energy landscapes |
| Q47658510 | Extending pressure-matching to inhomogeneous systems via local-density potentials |
| Q48056739 | Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions. |
| Q61811898 | Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT |
| Q48055259 | Getting excited: challenges in quantum-classical studies of excitons in polymeric systems. |
| Q51025338 | Heat conduction in nanoscale materials: a statistical-mechanics derivation of the local heat flux. |
| Q50319253 | Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water. |
| Q90324351 | Implementing efficient concerted rotations using Mathematica and C code⋆ |
| Q64074053 | Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure |
| Q38847957 | Improved accuracy of hybrid atomistic/coarse-grained simulations using reparametrised interactions |
| Q30617965 | In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation |
| Q48052727 | In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force. |
| Q36277912 | Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism |
| Q38764563 | Interactions and design rules for assembly of porous colloidal mesophases. |
| Q52677042 | IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. |
| Q30402437 | JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories |
| Q47989211 | Langevin-Poisson-EQT: A dipolar solvent based quasi-continuum approach for electric double layers. |
| Q48178417 | Local and global dynamics of multi-resolved polymer chains: Effects of the interactions atoms-beads on the dynamic of the chains |
| Q64285708 | Machine Learning of Coarse-Grained Molecular Dynamics Force Fields |
| Q47998413 | Martini Coarse-Grained Force Field: Extension to RNA. |
| Q35294264 | Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters |
| Q38836142 | Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. |
| Q58051716 | Modeling of Polymer Structure and Conformations in Polymer Nanocomposites from Atomistic to Mesoscale: A Review |
| Q38658585 | Modification of 56ACARBO force field for molecular dynamic calculations of chitosan and its derivatives |
| Q89701300 | Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations |
| Q37688779 | More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. |
| Q38957027 | Mori-Zwanzig theory for dissipative forces in coarse-grained dynamics in the Markov limit |
| Q92528023 | Multiconfigurational Coarse-Grained Molecular Dynamics |
| Q38974882 | Multiscale Modelling of Bionano Interface. |
| Q47161599 | OPUS-CSF: A C-atom-based scoring function for ranking protein structural models |
| Q57975273 | On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer |
| Q51027542 | On the calculation of internal forces in mechanically stressed polyatomic molecules. |
| Q41154585 | On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids |
| Q51569925 | On the representability problem and the physical meaning of coarse-grained models. |
| Q62599579 | Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes |
| Q62599580 | Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules |
| Q42022642 | Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides |
| Q38692056 | Perspective: Dissipative particle dynamics |
| Q47965131 | Phase behavior of patchy spheroidal fluids. |
| Q49494629 | Physical models of collective cell motility: from cell to tissue. |
| Q93195323 | Pitfalls of the Martini Model |
| Q41634502 | Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation |
| Q38712849 | Prediction of self-assemblies of sodium dodecyl sulfate and fragrance additives using coarse-grained force fields |
| Q36056772 | Protein folding guides disulfide bond formation |
| Q48047200 | Protein simulation using coarse-grained two-bead multipole force field with polarizable water models |
| Q38629307 | Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints |
| Q47227642 | Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM). |
| Q52653796 | Quantum theory of multiscale coarse-graining. |
| Q47235409 | RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. |
| Q92373510 | Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications |
| Q35699396 | Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA. |
| Q59223084 | STOCK: Structure mapper and online coarse-graining kit for molecular simulations |
| Q58048725 | Sampling large conformational transitions: adenylate kinase as a testing ground |
| Q38623521 | Sequence transferable coarse-grained model of amphiphilic copolymers. |
| Q35953946 | Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces |
| Q34337372 | Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems |
| Q33878711 | Structure and conformational dynamics of scaffolded DNA origami nanoparticles |
| Q51076841 | Structure of a tractable stochastic mimic of soft particles. |
| Q64264084 | Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites |
| Q50948155 | Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study. |
| Q50896330 | Systematic hierarchical coarse-graining with the inverse Monte Carlo method. |
| Q41005036 | Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits |
| Q48047632 | The "sugar" coarse-grained DNA model. |
| Q35590418 | The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems |
| Q50540926 | The derivation and approximation of coarse-grained dynamics from Langevin dynamics. |
| Q48048312 | The entropy of a complex molecule. |
| Q46030859 | The impact of resolution upon entropy and information in coarse-grained models. |
| Q41402303 | The intermolecular NOE is strongly influenced by dynamics |
| Q57368955 | The relative entropy is fundamental to adaptive resolution simulations |
| Q83232673 | The role of scaffold reshaping and disassembly in dynamin driven membrane fission |
| Q33693246 | Theoretical frameworks for multiscale modeling and simulation |
| Q33901748 | Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules |
| Q51081382 | Theory of non-equilibrium critical phenomena in three-dimensional condensed systems of charged mobile nanoparticles. |
| Q93005917 | Thermodynamics of a Compressible Maier-Saupe Model Based on the Self-Consistent Field Theory of Wormlike Polymer |
| Q47918895 | Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces |
| Q47780985 | Thermodynamics of star polymer solutions: A coarse-grained study |
| Q38406873 | Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect |
| Q40337321 | Transferability of the coarse-grained potentials for trans-1,4-polybutadiene |
| Q47321856 | Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. |
| Q42053563 | Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations |
| Q48046239 | Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins |
| Q91990826 | Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability |
| Q46575037 | Understanding and Designing the Gold-Bio Interface: Insights from Simulations |
| Q34489622 | cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA |
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