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Details of SAPdb ID 1633

Primary information
SAPdb_ID	1633
PMID	23795243
Year	2011
Name	VF
Sequence	VF
N-Terminal Modification	Free
C-Terminal Modification	Free
Non-terminal Modication	None
Length	2
Peptide/Conjugate/Mixture	Peptide
Conjugate Partner	None
Technique	Insilico method: MARTINI coarse - grained molecular dynamic
Solvent	Water
Method	A 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
Concentration	0.4M
pH	NA
Temperature	30 °C
Incubation Period	NA
Self-Assembly Formation	No
Type of Self-Assembly	None
Size of Self-Assembled structure	AP score: 1.8
Linear/Cyclic	Linear
Stability of Nanostructure	NA
Comment	NA
Secondary information
Physico-Chemical properties	Physico-Chemical properties
STRUCTURE	Predicted Structure
SMILES	N[C@@H](C(C)C)C(=O)N[C@@H](Cc1ccccc1)C=O