Patent Document ID: 8244504
Application ID: 12344192
Patent Flag: 1

Claim One:
1. A computerized method of calculating a free energy landscape of a molecular structure Distance Constraint Model using probability distributions predicting the presence of at least one proximity state and at least one body bar network representing an ensemble of constraint topologies, the method comprising: determining microscopic interaction types and proximity configurations of molecular constituents affecting thermodynamic properties of the molecular structure; calculating, for said at least one proximity state, a respective solvent entropy value, a respective solvent enthalpy value, and a respective conformational enthalpy value; calculating, for said at least one proximity state, a respective conformational entropy value, wherein calculating said respective conformational entropy value comprises the steps of (i) modeling constraints within the molecular structure using bars, wherein a probability that a bar is present (P) and a conditional probability for said bar to be an independent constraint (Q) are real numbers ranging from 0 to 1, and (ii) adding entropic contributions from bars representing independent constraints; selecting order parameters for constructing the free energy landscape, wherein groups of order parameters define nodes within the free energy landscape; determining, via a computer processor, a probability that a bar is present for said at least one proximity state; and calculating, via the computer processor, a minimum upper bound value for total free energy for a node in said proximity state, wherein said minimum upper bound value is based on P, Q, and the probability distribution for said proximity state, and wherein said minimum upper bound value for total free energy for said node is composed of a sum of said respective solvent entropy value, said respective solvent enthalpy value, said respective conformational enthalpy value and said respective conformational entropy value.