Simulation method for calculating the entropy and free energy of peptides and proteins

scholarly article

Simulation method for calculating the entropy and free energy of peptides and proteins is …
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scholarly articleQ13442814

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P819ADS bibcode2004PNAS..101.9241C
P356DOI10.1073/PNAS.0308201101
P932PMC publication ID438960
P698PubMed publication ID15197271
P5875ResearchGate publication ID8510845

P2093author name stringHagai Meirovitch
Srinath Cheluvaraja
P2860cites workEquation of State Calculations by Fast Computing MachinesQ5384234
Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR dataQ30579093
A simulation method for calculating the absolute entropy and free energy of fluids: application to liquid argon and waterQ35316024
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coilQ68020418
Stability of polypeptide conformational states as determined by computer simulation of the free energyQ69052607
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobinQ69706390
Computer simulation of the free energy of polymer chains with excluded volume and with finite interactionsQ77819303
Packing structures and transitions in liquids and solidsQ81031838
P433issue25
P407language of work or nameEnglishQ1860
P304page(s)9241-9246
P577publication date2004-06-14
P1433published inProceedings of the National Academy of Sciences of the United States of AmericaQ1146531
P1476titleSimulation method for calculating the entropy and free energy of peptides and proteins
P478volume101

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cites work (P2860)
Q31158725A black-box re-weighting analysis can correct flawed simulation data
Q36601750A simplified confinement method for calculating absolute free energies and free energy and entropy differences
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Q33463565Absolute free energies estimated by combining precalculated molecular fragment libraries
Q43297790Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces
Q40441735Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides
Q42587806Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force
Q40306265Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method
Q41868273Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method
Q28391435Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide
Q42180577Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins
Q28394305Equilibrium sampling in biomolecular simulations
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Q28386158Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space
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Q41497542Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids
Q34562935Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping
Q42439664Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
Q39958434Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics
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Q28390933Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects
Q30477360Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae

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