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Details of SAPdb entry with Sequence WY
Primary information
SAPdb ID 1630,
PMID23795243
Peptide NameWY
Peptide sequenceWY
N-Terminal ModificationFree
C-Terminal ModificationFree
Non-Terminal ModificationNone
Length2
Peptide/ConjuagatePeptide
Conjugate partnerNone
TechniqueInsilico method: MARTINI coarse - grained molecular dynamic
SolventWater
MethodA simulation for each dipeptide (in their zwitterionic form) was set up using the GROMACS molecular dynamics package. A cubic box with 300 dipeptides, placed randomly with a minimum distance of 3 Å between them, was solvated in standard MARTINI CG water (four water molecules per bead) to a final concentration of ∼0.4 M. A Berendsen thermostat and barostat36 were used to keep the temperature at 303 K and pressure at 1 bar, respectively. Bond lengths in aromatic side chains and the backbone side-chain bonds in I, V, and Y were constrained using the LINCS algorithm.37 All boxes were energy minimized using the steepest descent integrator and then equilibrated for 4 106 time steps of 25 fs. The total screening simulation time equates to 100 ns, but because of the smoothness of the CG potentials, this roughly equates to an effective 400 ns of atomistic simulation time
Conc0.4M
Temperature30 °C
Year2011
Self assemblyYes
Type of Self assemblyAggregate
Tertiary Structure
(Technique)		Not Predicted),
Linear
NA
NA
Other
NA
WY
N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](Cc1ccc(O)cc1)C=O