This page describes the method we develop for solving the inverse protein folding problem.

Our protein sequence design uses a Monte Carlo search technique in sequence space, a SCMF technique in structure space, and the Random Energy Model for reaching specificity. [1]

Schematic description of our Monte Carlo protein sequence design procedure.
Starting from a random sequence, S0, of the required composition, a model structure is built,
and its energy is evaluated and stored as E0. Two positions are then chosen at random,
and the corresponding amino acid types in S0 are exchanged, yielding a new sequence S1.
A new model structure is built based on S1, and its energy is stored as E1. The sequence move from S0 to S1
is accepted or rejected according to the Metropolis Monte Carlo probability The procedure is repeated
until the system has equilibrated and the energy remains steady.

References