Patent ID: 7925484

Claim:
A method to predict the topology of the spatial arrangement of an amino acid sequence comprising: using an entropy evaluation model that takes into account the global contributions of entropy to the folding of a protein (herein referred to by the name cross linking entropy (CLE) model) combined with other thermodynamic potentials as a protein-folding model to predict said topology, wherein using said entropy evaluation model to predict said topology comprises the following steps: A. inputting an amino acid sequence of said protein, B. preparing information on secondary structure of said amino acid sequence by way of at least one theoretical or experimental estimate, C. applying the CLE model to said amino acid sequence and secondary structure information to evaluate the free energy of a combinatorial number of β-strand and α-helix arrangements performed in polynomial time defined by c(n−1)(n+1) wherein c is a constant and n is the number of secondary structure elements found in said amino acid in step A and prepared in step B, D. applying the CLE model in conjunction with other thermodynamic potentials that approximate hydrophobic, electrostatic and polar interactions in a thermodynamic calculation to account for both short and long range folding interactions and predict a minimum free energy and corresponding topology of the said amino acid sequence, E. applying the CLE model to predict the global folding kinetics information of said amino acid sequence, and F. storing the global folding kinetics information in a data file or in other form of digital memory, wherein steps A. through F. are performed with a computer.