| scholarly article | Q13442814 |
| P356 | DOI | 10.1007/S00894-014-2306-5 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1007/s00894-014-2306-5 |
| P932 | PMC publication ID | 4139597 |
| P698 | PubMed publication ID | 25024008 |
| P5875 | ResearchGate publication ID | 263971151 |
| P50 | author | Harold A. Scheraga | Q15432669 |
| Magdalena A Mozolewska | Q88044586 | ||
| Adam K Sieradzan | Q89269081 | ||
| Tomasz K Wirecki | Q101470860 | ||
| Mariusz Makowski | Q123598452 | ||
| Cezary Czaplewski | Q55117909 | ||
| Adam Liwo | Q56937795 | ||
| Stanislaw Oldziej | Q58002558 | ||
| Maciej Maciejczyk | Q62027544 | ||
| Rafal Slusarz | Q73383757 | ||
| P2093 | author name string | Yi He | |
| Yanping Yin | |||
| Maciej Baranowski | |||
| Bartłomiej Zaborowski | |||
| Paweł Krupa | |||
| Andrei Niadzvedtski | |||
| Dawid Jagieła | |||
| Ewa Gołaś | |||
| P2860 | cites work | The Protein Data Bank | Q24515306 |
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| Accelerating molecular dynamic simulation on graphics processing units | Q24654186 | ||
| Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones | Q27683212 | ||
| Atomic-level characterization of the structural dynamics of proteins | Q29616380 | ||
| 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 | ||
| Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field | Q36881617 | ||
| Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode | Q36927066 | ||
| Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems | Q36930272 | ||
| Coarse-grained models of protein folding: toy models or predictive tools? | Q37045351 | ||
| Minimal models for proteins and RNA from folding to function | Q37361859 | ||
| Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field | Q37383879 | ||
| Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains | Q37385231 | ||
| Simulating DNA at low resolution | Q41052965 | ||
| Coarse-grained model for simulation of RNA three-dimensional structures. | Q41688309 | ||
| Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins | Q42958513 | ||
| Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation | Q43018771 | ||
| Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA. | Q45221932 | ||
| Coarse-grained simulations of RNA and DNA duplexes | Q45894084 | ||
| Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose. | Q45982643 | ||
| Correcting for heat capacity and 5'-TA type terminal nearest neighbors improves prediction of DNA melting temperatures using nearest-neighbor thermodynamic models | Q46666960 | ||
| Discrete molecular dynamics simulations of peptide aggregation | Q47415818 | ||
| The MARTINI Coarse-Grained Force Field: Extension to Proteins. | Q47741405 | ||
| Statistical mechanics of a nonlinear model for DNA denaturation | Q74495460 | ||
| Multiscale modeling of lipids and lipid bilayers | Q81141978 | ||
| Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains | Q81567951 | ||
| Peptide folding using multiscale coarse-grained models | Q82025586 | ||
| Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model | Q83503460 | ||
| How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics? | Q84358096 | ||
| Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling | Q84843927 | ||
| Exploration of transferability in multiscale coarse-grained peptide models | Q84924686 | ||
| HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA | Q84959270 | ||
| The MARTINI force field: coarse grained model for biomolecular simulations | Q29617215 | ||
| Protein structure prediction by global optimization of a potential energy function. | Q30322315 | ||
| Recent improvements in prediction of protein structure by global optimization of a potential energy function. | Q30327941 | ||
| Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. | Q30350721 | ||
| Lessons from application of the UNRES force field to predictions of structures of CASP10 targets | Q30353196 | ||
| Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. | Q30356003 | ||
| Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. | Q30359025 | ||
| Martini Coarse-Grained Force Field: Extension to Carbohydrates. | Q30381806 | ||
| Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field. | Q30382147 | ||
| Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II | Q30383562 | ||
| Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field | Q30385785 | ||
| Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. | Q30387121 | ||
| Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation | Q30402159 | ||
| Coarse-grained force field: general folding theory | Q30403444 | ||
| The coarse-grained OPEP force field for non-amyloid and amyloid proteins. | Q30418632 | ||
| Kinks, loops, and protein folding, with protein A as an example | Q30566698 | ||
| PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides | Q30577456 | ||
| RNA 3D structure prediction by using a coarse-grained model and experimental data | Q30593882 | ||
| Mechanical unfolding of RNA hairpins | Q33784317 | ||
| Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains | Q33849857 | ||
| Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field | Q34311672 | ||
| PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics | Q34432049 | ||
| Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains | Q34978512 | ||
| Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains | Q34996988 | ||
| The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems | Q35590418 | ||
| A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)) | Q35609533 | ||
| Hidden protein folding pathways in free-energy landscapes uncovered by network analysis | Q36036240 | ||
| Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics | Q36050078 | ||
| Coarse-grained models for proteins | Q36101080 | ||
| Coexistence of phases in a protein heterodimer | Q36139267 | ||
| Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide | Q36277693 | ||
| Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine | Q36329551 | ||
| Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding | Q36590747 | ||
| Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain | Q36651989 | ||
| A coarse grain model for DNA. | Q51053784 | ||
| Coarse-grained model of nucleic acid bases. | Q51614529 | ||
| DNA nanotweezers studied with a coarse-grained model of DNA. | Q51696669 | ||
| Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. | Q51927646 | ||
| Anton, a special-purpose machine for molecular dynamics simulation | Q56019494 | ||
| THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Q56157177 | ||
| Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species | Q57752459 | ||
| Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics | Q57795101 | ||
| Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent | Q57835665 | ||
| Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test | Q57906164 | ||
| Coarse-grained force field for the nucleosome from self-consistent multiscaling | Q58022441 | ||
| Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix | Q59278286 | ||
| Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains | Q59278299 | ||
| Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins | Q59278305 | ||
| Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization | Q59278306 | ||
| Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems† | Q59278307 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 8 | |
| P921 | main subject | macromolecule | Q178593 |
| P304 | page(s) | 2306 | |
| P577 | publication date | 2014-07-15 | |
| P1433 | published in | Journal of Molecular Modeling | Q1709860 |
| P1476 | title | A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions | |
| P478 | volume | 20 |
| Q47895931 | A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains |
| Q48053335 | A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains |
| Q57280872 | A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields |
| Q49615824 | A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. |
| Q90380555 | Assessment of chemical-crosslink-assisted protein structure modeling in CASP13 |
| Q65001278 | CABS-flex standalone: a simulation environment for fast modeling of protein flexibility. |
| Q93054243 | Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation |
| Q90131372 | Computer simulations of protein-membrane systems |
| Q47757235 | Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins |
| Q55027423 | Extension of coarse-grained UNRES force field to treat carbon nanotubes. |
| Q52314279 | Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase. |
| Q58799743 | Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners |
| Q50959023 | Introduction of steered molecular dynamics into UNRES coarse-grained simulations package. |
| Q58607124 | Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models |
| Q30757204 | Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction |
| Q30390128 | Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. |
| Q47405976 | Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information |
| Q92373510 | Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications |
| Q60920804 | Reoptimized UNRES Potential for Protein Model Quality Assessment |
| Q51521028 | Role of the sulfur to α-carbon thioether bridges in thurincin H. |
| Q100958586 | Sampling of the conformational landscape of small proteins with Monte Carlo methods |
| Q48051336 | Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains |
| Q47389316 | Structures of Dynamic Protein Complexes: Hybrid Techniques to Study MAP Kinase Complexes and the ESCRT System |
| Q55518838 | UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. |
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