scholarly article | Q13442814 |
P2093 | author name string | Carlos Simmerling | |
Asim Okur | |||
Viktor Hornak | |||
Lauren Wickstrom | |||
Daniel R Roe | |||
P2860 | cites work | Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. | Q52224995 |
Comparative study of generalized born models: Born radii and peptide folding | Q79935286 | ||
Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model | Q86839623 | ||
Tryptophan zippers: Stable, monomeric -hairpins | Q27631564 | ||
VMD: visual molecular dynamics | Q27860554 | ||
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features | Q27860675 | ||
The Amber biomolecular simulation programs | Q27860745 | ||
Comparison of multiple Amber force fields and development of improved protein backbone parameters | Q27861040 | ||
Solvent viscosity dependence of the folding rate of a small protein: distributed computing study | Q28187900 | ||
Free energy landscape of protein folding in water: Explicit vs. implicit solvent | Q28205750 | ||
Effective Born radii in the generalized Born approximation: the importance of being perfect | Q28221237 | ||
Implicit solvent models | Q28267646 | ||
Classical electrostatics in biology and chemistry | Q29615082 | ||
Exploring protein native states and large-scale conformational changes with a modified generalized born model | Q29617088 | ||
Unfolded state of polyalanine is a segmented polyproline II helix. | Q30341342 | ||
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method | Q30969801 | ||
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent | Q33713877 | ||
Polyproline II structure in a sequence of seven alanine residues. | Q34034318 | ||
Generalized born models of macromolecular solvation effects | Q34059768 | ||
Hydration dynamics near a model protein surface. | Q34185121 | ||
Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? | Q34189756 | ||
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. | Q34478711 | ||
Recent advances in the development and application of implicit solvent models in biomolecule simulations | Q35749514 | ||
Improving implicit solvent simulations: a Poisson-centric view | Q36101076 | ||
Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions | Q44854320 | ||
Incorporating variable dielectric environments into the generalized Born model | Q44909942 | ||
A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution | Q46188365 | ||
Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field | Q46225929 | ||
Accelerated Poisson-Boltzmann calculations for static and dynamic systems | Q46543722 | ||
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model | Q47307353 | ||
Polyproline II helix is the preferred conformation for unfolded polyalanine in water | Q47715263 | ||
Investigation of Salt Bridge Stability in a Generalized Born Solvent Model. | Q51295899 | ||
P433 | issue | 7 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | bias | Q742736 |
P1104 | number of pages | 12 | |
P304 | page(s) | 1846-1857 | |
P577 | publication date | 2007-01-27 | |
P1433 | published in | Journal of Physical Chemistry B | Q668669 |
P1476 | title | Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation | |
P478 | volume | 111 |
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