| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcc/VitalisP09 |
| P356 | DOI | 10.1002/JCC.21005 |
| P932 | PMC publication ID | 2670230 |
| P698 | PubMed publication ID | 18506808 |
| P5875 | ResearchGate publication ID | 5343740 |
| P2093 | author name string | Andreas Vitalis | |
| Rohit V Pappu | |||
| P2860 | cites work | Electrostatics of nanosystems: application to microtubules and the ribosome | Q24555224 |
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| A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G | Q27651724 | ||
| All-atom empirical potential for molecular modeling and dynamics studies of proteins | Q27860468 | ||
| Structure validation by Calpha geometry: phi,psi and Cbeta deviation | Q27860657 | ||
| Effective energy function for proteins in solution | Q28142746 | ||
| Evaluation of a fast implicit solvent model for molecular dynamics simulations | Q28211559 | ||
| Effective Born radii in the generalized Born approximation: the importance of being perfect | Q28221237 | ||
| A short linear peptide that folds into a native stable beta-hairpin in aqueous solution | Q28295200 | ||
| Why are "natively unfolded" proteins unstructured under physiologic conditions? | Q29615739 | ||
| A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 | Q29617517 | ||
| On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. | Q30333244 | ||
| Exploring peptide energy landscapes: a test of force fields and implicit solvent models. | Q30343068 | ||
| Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". | Q30350444 | ||
| Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration | Q30422341 | ||
| Synthetic protein design: construction of a four-stranded beta-sheet structure and evaluation of its integrity in methanol-water systems | Q30620254 | ||
| On the interpretation of biochemical data by molecular dynamics computer simulation | Q30974251 | ||
| Intrinsic backbone preferences are fully present in blocked amino acids | Q31030110 | ||
| Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions | Q31072074 | ||
| Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi | Q31140155 | ||
| The complete folding pathway of a protein from nanoseconds to microseconds | Q33186113 | ||
| Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent | Q33713877 | ||
| Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds | Q34014321 | ||
| The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation | Q34037348 | ||
| A linear lattice model for polyglutamine in CAG-expansion diseases | Q34153913 | ||
| Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation | Q34154622 | ||
| Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. | Q46136993 | ||
| Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures | Q46426339 | ||
| Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins | Q46662533 | ||
| Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model | Q47307353 | ||
| Design of a 20-amino acid, three-stranded beta-sheet protein | Q47625414 | ||
| Electrostatic effects in macromolecules: fundamental concepts and practical modeling | Q47959634 | ||
| Solvation free energy of amino acids and side-chain analogues. | Q51075650 | ||
| Characterizing the conformational ensemble of monomeric polyglutamine. | Q51317035 | ||
| Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints. | Q51565121 | ||
| Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. | Q51633889 | ||
| Application of the diffusion-collision model to the folding of three-helix bundle proteins. | Q51641193 | ||
| Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution | Q52008690 | ||
| Generalized born model with a simple smoothing function. | Q52009475 | ||
| AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. | Q54640063 | ||
| Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide | Q56903634 | ||
| Limitations of atom-centered dielectric functions in implicit solvent models | Q57133539 | ||
| Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method | Q57133763 | ||
| Distance and exposure dependent effective dielectric function | Q57134702 | ||
| The effects of guanidine hydrochloride on the 'random coil' conformations and NMR chemical shifts of the peptide series GGXGG | Q57908623 | ||
| Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors | Q79559995 | ||
| Implicit solvent simulations of DPC micelle formation | Q79941720 | ||
| Exploring the helix-coil transition via all-atom equilibrium ensemble simulations | Q34189691 | ||
| Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? | Q34189756 | ||
| Macromolecular electrostatics: continuum models and their growing pains | Q34215908 | ||
| Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures | Q34280282 | ||
| Interfaces and the driving force of hydrophobic assembly | Q34455286 | ||
| Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms | Q34694062 | ||
| Hydration theory for molecular biophysics | Q34989915 | ||
| End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation | Q35033709 | ||
| Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation | Q35566520 | ||
| Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties | Q35574706 | ||
| Ionic effects beyond Poisson-Boltzmann theory | Q35687365 | ||
| Recent advances in the development and application of implicit solvent models in biomolecule simulations | Q35749514 | ||
| Molecular picture of folding of a small alpha/beta protein | Q35873286 | ||
| Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories | Q35963371 | ||
| Improving implicit solvent simulations: a Poisson-centric view | Q36101076 | ||
| Structural studies of the engrailed homeodomain | Q36278322 | ||
| Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol | Q36279587 | ||
| De novo design of a monomeric three-stranded antiparallel beta-sheet | Q36281494 | ||
| Alanine is helix-stabilizing in both template-nucleated and standard peptide helices | Q36448925 | ||
| Beta-structures in fibrous proteins. | Q36693047 | ||
| Electrostatic screening of charge and dipole interactions with the helix backbone | Q36780118 | ||
| Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model | Q36871997 | ||
| Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. | Q37356463 | ||
| Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures | Q38329419 | ||
| Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations | Q40297191 | ||
| Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling | Q40439944 | ||
| Rate of beta-structure formation in polypeptides | Q42159713 | ||
| Salting the charged surface: pH and salt dependence of protein G B1 stability | Q42183744 | ||
| Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments | Q42836335 | ||
| Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment | Q43014694 | ||
| Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide | Q43904611 | ||
| Solution structure of polyglutamine tracts in GST-polyglutamine fusion proteins | Q43923832 | ||
| Calculation of the free energy of solvation for neutral analogs of amino acid side chains | Q43956197 | ||
| Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution | Q44296010 | ||
| Effective energy function for proteins in lipid membranes | Q44496100 | ||
| Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants | Q44580868 | ||
| Accuracy of free energies of hydration using CM1 and CM3 atomic charges | Q44927750 | ||
| Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides. | Q45931992 | ||
| Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation | Q46099457 | ||
| P433 | issue | 5 | |
| P304 | page(s) | 673-699 | |
| P577 | publication date | 2009-04-01 | |
| P1433 | published in | Journal of Computational Chemistry | Q3186908 |
| P1476 | title | ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions | |
| P478 | volume | 30 |
| Q88015627 | A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain |
| Q90727042 | A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain |
| Q64079926 | A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair |
| Q34144086 | A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences |
| Q28681184 | A decade and a half of protein intrinsic disorder: biology still waits for physics |
| Q37048844 | A quantitative measure for protein conformational heterogeneity |
| Q33922028 | A simple molecular mechanics integrator in mixed rigid body and dihedral angle space |
| Q35128365 | A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent |
| Q88150475 | An Extended Guinier Analysis for Intrinsically Disordered Proteins |
| Q94481584 | An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins |
| Q35379375 | Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings |
| Q96769244 | Aromatic interactions with membrane modulate human BK channel activation |
| Q33761386 | Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization |
| Q26853115 | Biomolecular electrostatics and solvation: a computational perspective |
| Q36277923 | CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences |
| Q22061736 | Classification of intrinsically disordered regions and proteins |
| Q47621056 | Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein. |
| Q47184120 | Concerted millisecond timescale dynamics in the intrinsically disordered carboxyl terminus of γ-tubulin induced by mutation of a conserved tyrosine residue. |
| Q36420850 | Conformation and Dynamics of the Troponin I C-Terminal Domain: Combining Single-Molecule and Computational Approaches for a Disordered Protein Region |
| Q36388382 | Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields. |
| Q34360837 | Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues |
| Q30009072 | Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck. |
| Q39432831 | Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods |
| Q47403167 | Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor |
| Q92185964 | Covalently-assembled single-chain protein nanostructures with ultra-high stability |
| Q36930963 | Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling |
| Q41293169 | Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements |
| Q33818465 | Describing sequence-ensemble relationships for intrinsically disordered proteins |
| Q34183931 | Differential geometry based solvation model I: Eulerian formulation |
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| Q27305237 | Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study |
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| Q34300832 | Ebola virus VP24 targets a unique NLS binding site on karyopherin alpha 5 to selectively compete with nuclear import of phosphorylated STAT1. |
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| Q47352295 | HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations |
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| Q30516044 | Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. |
| Q59332309 | Inferring properties of disordered chains from FRET transfer efficiencies |
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| Q40266179 | Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA. |
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| Q89876186 | Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6 |
| Q55044856 | Looking at the Disordered Proteins through the Computational Microscope. |
| Q56531407 | Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments |
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| Q64273327 | Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields |
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