Alchemical free energy calculations and multiple conformational substates

scientific article published in February 2005

Alchemical free energy calculations and multiple conformational substates is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1063/1.1850900
P698PubMed publication ID15836022

P50authorChristian SchröderQ42320710
Stefan BoreschQ50104475
P2093author name stringMartin Leitgeb
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Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulationsQ30885021
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetaseQ32124412
The statistical-thermodynamic basis for computation of binding affinities: a critical reviewQ33915676
COMPUTING: Screen Savers of the World Unite!Q34670167
Free energy simulations come of age: protein-ligand recognitionQ34691182
Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculationsQ36279120
Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnaseQ37637250
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsinQ44833188
Accelerated molecular dynamics: a promising and efficient simulation method for biomoleculesQ46058456
Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutantQ50150501
Replica-exchange molecular dynamics method for protein foldingQ55879366
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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteinsQ56776034
The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical ResultsQ57831761
Multidimensional replica-exchange method for free-energy calculationsQ57906232
Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensembleQ57906319
Affinities of amino acid side chains for solvent waterQ57948314
Enhanced Configurational Sampling in Binding Free-Energy CalculationsQ58849213
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P433issue8
P407language of work or nameEnglishQ1860
P304page(s)84109
P577publication date2005-02-01
P1433published inJournal of Chemical PhysicsQ900472
P1476titleAlchemical free energy calculations and multiple conformational substates
P478volume122

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cites work (P2860)
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Q27334812Computational study of synthetic agonist ligands of ionotropic glutamate receptors
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Q45179200Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy
Q51887454Exploring a free energy landscape by means of multidimensional infrared and terahertz spectroscopies.
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Q51604998Let's get honest about sampling.
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