Molecular dynamics simulations

Current Opinion in Structural Biology

Volumn 12, Issue 2, 2002, Pages 190-196

  Hansson, Tomas ^a   Oostenbrink, Chris ^a   Van Gunsteren, WilfredF ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

PRION PROTEIN;

ALPHA HELIX; CALCULATION; COMPUTER SIMULATION; MEMBRANE CHANNEL; METHODOLOGY; MOLECULAR DYNAMICS; PH; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW;

EID: 0036536428     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00308-1     Document Type: Review

References (68)

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4. An improved empirical potential energy function for molecular simulations of phospholipids
5. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
6. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
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8. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
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13. IBM promises scientists 500-fold leap in supercomputing power and a chance to tackle protein structure
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33. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
34. Prediction of a ligand-induced conformational change in the catalytic core of Cdc25A
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50. Computational analysis of binding of P1 variants to trypsin
51. Sensitivity of an empirical affinity scoring function to changes in receptor-ligand complex conformations
52. Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach
53. Theoretical studies suggest a new antifolate as a more potent inhibitor of thymidylate synthase
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55. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efavirenz by docking and MM-PBSA
56. Structural basis of binding of high-affinity ligands to protein kinase C: Prediction of the binding modes through a new molecular dynamics method and evaluation by site-directed mutagenesis
57. Electrostatic free energy calculations for macromolecules: A hybrid molecular dynamics/continuum electrostatics approach
58. Molecular dynamics simulation of the kinetics of spontaneous micelle formation
59. Molecular dynamics simulations of antimicrobial peptides: From membrane binding to transmembrane channels
60. Molecular dynamics simulation of adrenocorticotropin (1-10) peptide in a solvated dodecylphosphocholine micelle
61. Molecular dynamics simulation of the structure of dimyristoylphosphatidylcholine bilayers with cholesterol, ergosterol, and lanosterol
62. Molecular dynamics study of bacteriorhodopsin and the purple membrane
63. The potassium channel: Structure, selectivity and diffusion
64. Ion permeation mechanism of the potassium channel
65. + channel in a bilayer membrane
66. Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL channel
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68. + channel