| scholarly article | Q13442814 |
| P819 | ADS bibcode | 2002PNAS...99.2782G |
| P356 | DOI | 10.1073/PNAS.042496899 |
| P932 | PMC publication ID | 122425 |
| P698 | PubMed publication ID | 11867710 |
| P5875 | ResearchGate publication ID | 11493927 |
| P50 | author | Karissa Sanbonmatsu | Q63190411 |
| Angel E. García | Q89238894 | ||
| P2860 | cites work | Comparison of simple potential functions for simulating liquid water | Q26778447 |
| Transient UV Raman spectroscopy finds no crossing barrier between the peptide alpha-helix and fully random coil conformation | Q30689216 | ||
| Helix nucleation kinetics from molecular simulations in explicit solvent | Q30969625 | ||
| Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design | Q34376818 | ||
| The mechanism of alpha-helix formation by peptides | Q35836992 | ||
| Interaction between water and polar groups of the helix backbone: an important determinant of helix propensities | Q36333304 | ||
| Electrostatic screening of charge and dipole interactions with the helix backbone | Q36780118 | ||
| Fast events in protein folding: helix melting and formation in a small peptide. | Q36789506 | ||
| Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model | Q36871997 | ||
| Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. | Q36885424 | ||
| Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities | Q37260438 | ||
| Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides | Q37281519 | ||
| Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. | Q41676098 | ||
| Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. | Q42244726 | ||
| Unfolding of an ?-helix in water | Q44974805 | ||
| Molecular dynamics simulations of helix denaturation | Q47637533 | ||
| Reversible peptide folding in solution by molecular dynamics simulation | Q47812843 | ||
| Elucidating the folding problem of helical peptides using empirical parameters. | Q52376869 | ||
| Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. | Q52447787 | ||
| Conformational studies of poly-L-alanine in water. | Q54602751 | ||
| Replica-exchange molecular dynamics method for protein folding | Q55879366 | ||
| A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules | Q55918670 | ||
| Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains | Q56522033 | ||
| Internal stark effect measurement of the electric field at the amino terminus of an alpha helix | Q57137999 | ||
| Molecular dynamics with coupling to an external bath | Q57569060 | ||
| Conformational Diffusion and Helix Formation Kinetics | Q57875246 | ||
| Computer simulation of aqueous Na-Cl electrolytes | Q57875620 | ||
| Ion pair potentials-of-mean-force in water | Q57875634 | ||
| Analysis of the heat capacity dependence of protein folding | Q67559643 | ||
| Side chain contributions to the stability of alpha-helical structure in peptides | Q68598333 | ||
| Water-inserted alpha-helical segments implicate reverse turns as folding intermediates | Q69633330 | ||
| Nanosecond time scale folding dynamics of a pentapeptide in water | Q70176155 | ||
| Exploring the energy landscape of a beta hairpin in explicit solvent | Q73379963 | ||
| Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations | Q74452346 | ||
| P433 | issue | 5 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 2782-2787 | |
| P577 | publication date | 2002-02-26 | |
| P1433 | published in | Proceedings of the National Academy of Sciences of the United States of America | Q1146531 |
| P1476 | title | Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds | |
| P478 | volume | 99 |
| Q36118923 | A Folding Pathway Model of Mini-Protein BBA5 |
| Q30830738 | A closer look into the α-helix basin |
| Q34771965 | A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. |
| Q34350851 | A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations |
| Q34187126 | A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory |
| Q30369376 | A test on peptide stability of AMBER force fields with implicit solvation |
| Q37161084 | ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions |
| Q92860154 | Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water |
| Q55344924 | Acidity and basicity interplay in amide and imide self-association. |
| Q30427576 | Alchemical free energy methods for drug discovery: progress and challenges |
| Q51890815 | All-atom level direct folding simulation of a betabetaalpha miniprotein. |
| Q34306895 | All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics |
| Q36043816 | An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution |
| Q42538477 | An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface |
| Q47969246 | An analytical study of the interplay between geometrical and energetic effects in protein folding |
| Q41478788 | An effective all-atom potential for proteins |
| Q31154422 | Are current molecular dynamics force fields too helical? |
| Q47822596 | Atomic simulations of protein folding, using the replica exchange algorithm. |
| Q34183483 | Atomically Detailed Simulations of Helix Formation with the Stochastic Difference Equation |
| Q42586074 | Automated Optimization of Potential Parameters |
| Q46474092 | Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics |
| Q30915666 | Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water |
| Q42929260 | Can Peptide Folding Simulations Provide Predictive Information for Aggregation Propensity? |
| Q58846433 | Chapter 7 Empirical Force Fields for Proteins: Current Status and Future Directions |
| Q41829181 | Circular dichroism and ultraviolet resonance Raman indicate little Arg-Glu side chain α-helix peptide stabilization |
| Q51571593 | Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants. |
| Q27861040 | Comparison of multiple Amber force fields and development of improved protein backbone parameters |
| Q58104780 | Computational Studies of Intrinsically Disordered Proteins |
| Q30385837 | Computational analysis of the CB1 carboxyl-terminus in the receptor-G protein complex |
| Q57657555 | Computational approach to unravel the impact of missense mutations of proteins (D2HGDH and IDH2) causing D-2-hydroxyglutaric aciduria 2 |
| Q57951622 | Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides |
| Q36344939 | Conformational sampling of peptides in cellular environments |
| Q42207188 | Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles |
| Q46099566 | Contribution of arginine-glutamate salt bridges to helix stability |
| Q57905888 | Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term |
| Q33603629 | Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment |
| Q51961150 | Convergence of replica exchange molecular dynamics. |
| Q39847711 | Coupling of replica exchange simulations to a non-Boltzmann structure reservoir |
| Q57905898 | Determination method of the balance of the secondary-structure-forming tendencies of force fields |
| Q38670843 | Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding |
| Q35022251 | Direct assessment of the α-helix nucleation time |
| Q36869856 | Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif |
| Q34845256 | Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein |
| Q36157560 | Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein |
| Q47299318 | Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations |
| Q50615279 | Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states. |
| Q34350548 | Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape |
| Q40307709 | Equilibrium structure and folding of a helix-forming peptide: circular dichroism measurements and replica-exchange molecular dynamics simulations |
| Q37428386 | Error and efficiency of replica exchange molecular dynamics simulations |
| Q33649931 | Error and efficiency of simulated tempering simulations |
| Q48058205 | Evaluating amber force fields using computed NMR chemical shifts. |
| Q46548564 | Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide |
| Q33564099 | Evaluating molecular mechanical potentials for helical peptides and proteins |
| Q51939839 | Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides. |
| Q44264791 | ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations |
| Q36104127 | Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution |
| Q33713782 | Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. |
| Q34189691 | Exploring the helix-coil transition via all-atom equilibrium ensemble simulations |
| Q40216639 | Extent of hydrogen-bond protection in folded proteins: a constraint on packing architectures |
| Q33713679 | Folding a protein in a computer: An atomic description of the folding/unfolding of protein A |
| Q35163087 | Folding and misfolding of the papillomavirus E6 interacting peptide E6ap |
| Q41902732 | Folding and unfolding of gammaTIM monomers and dimers |
| Q30164860 | Folding of a highly conserved diverging turn motif from the SH3 domain |
| Q36717653 | Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects |
| Q40319333 | Folding thermodynamics of peptides |
| Q36458088 | Force field influences in beta-hairpin folding simulations |
| Q35590728 | Force fields for protein simulations |
| Q28205750 | Free energy landscape of protein folding in water: Explicit vs. implicit solvent |
| Q30368713 | Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. |
| Q36426407 | Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains |
| Q44253114 | Helix-coil transitions re-visited |
| Q58454459 | Hydrophobic interactions in the formation of secondary structures in small peptides |
| Q37659025 | Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide |
| Q57905829 | Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion |
| Q83742288 | Influence of an unnatural amino acid side chain on the conformational dynamics of peptides |
| Q78968479 | Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L |
| Q56970630 | Intramolecular modulation of electric fields in folding proteins |
| Q91034175 | Intraresidual Correlated Motions in Peptide Chains |
| Q100387314 | Investigating the structural impacts of a novel missense variant identified with whole exome sequencing in an Egyptian patient with propionic acidemia |
| Q47714083 | Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides |
| Q36666656 | K+/Na+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints |
| Q42145390 | Kinetics of helix unfolding: molecular dynamics simulations with milestoning |
| Q46257808 | Kinetics of the coil-to-helix transition on a rough energy landscape. |
| Q35910677 | Local structure formation in simulations of two small proteins |
| Q35607904 | Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices |
| Q48048113 | Microscopic nucleation and propagation rates of an alanine-based α-helix. |
| Q36501036 | Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. |
| Q40316502 | Misfolding pathways of the prion protein probed by molecular dynamics simulations |
| Q51436533 | Mixed Monte Carlo/molecular dynamics simulations in explicit solvent. |
| Q42697889 | Mixed-salt effects on the conformation of a short salt-bridge-forming α helix: a simulation study. |
| Q36722325 | Modified replica exchange simulation methods for local structure refinement |
| Q39714826 | Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana. |
| Q30581118 | Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields |
| Q34190144 | Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent |
| Q51303943 | Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis. |
| Q43088941 | Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics. |
| Q35315878 | Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements |
| Q44063793 | New force field on modeling intrinsically disordered proteins. |
| Q30386400 | On potential energy models for EA-based ab initio protein structure prediction. |
| Q57905919 | Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank |
| Q33465189 | Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides |
| Q40317625 | Penetratin-membrane association: W48/R52/W56 shield the peptide from the aqueous phase. |
| Q47749949 | Peptide dimerization-dissociation rates from replica exchange molecular dynamics |
| Q51877373 | Peptide folding kinetics from replica exchange molecular dynamics. |
| Q46221579 | Preserving the Boltzmann ensemble in replica-exchange molecular dynamics |
| Q36610875 | Protective V127 prion variant prevents prion disease by interrupting the formation of dimer and fibril from molecular dynamics simulations |
| Q46172362 | Protonation Enhances the Inherent Helix-Forming Propensity of pHLIP. |
| Q41972949 | Psi-constrained simulations of protein folding transition states: implications for calculating |
| Q42552862 | Quantifying the structural requirements of the folding transition state of protein A and other systems |
| Q36389629 | Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification |
| Q33862294 | Relationship between side chain structure and 14-helix stability of beta3-peptides in water |
| Q35843475 | Residue-specific α-helix propensities from molecular simulation |
| Q34183582 | Role of Backbone Hydration and Salt-Bridge Formation in Stability of α-Helix in Solution |
| Q42411748 | Salt dependence of an alpha-helical peptide folding energy landscapes |
| Q28546876 | Secondary Structure of Rat and Human Amylin across Force Fields |
| Q33713877 | Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent |
| Q33784348 | Simulations of the pressure and temperature unfolding of an alpha-helical peptide. |
| Q33694936 | Simulations of the role of water in the protein-folding mechanism |
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| Q52591449 | Stochastic gating and drug-ribosome interactions. |
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