PATENT CLAIM ANALYSIS

Application Number: 16045366
Application Type: Utility
Filing Date: 2018-07
Publication Date: 2019-01
Patent Classification: ["703", "011000"]

Abstract:
Methods for assessing the consistency and reliability of the calculations using cycle closures in relative binding free energy calculation paths. The methods are used for determining relative strength of binding between a receptor and individual members of a set ligands to form complexes between individual ligand set members and the receptor, in which the binding free energy difference with the lowest error is determined by probabilistic determination of the free energy differences and error distributions about those differences along each of the legs of the closed thermodynamic cycle that probabilistically lead to the hysteresis(es) value(s) observed for each closed of the closed thermodynamic cycle.

Claim (Index 2):
A structure-based drug design method, comprising:\n identifying a protein target of pharmacological interest; identifying a plurality of ligands for binding to the protein; for each of the plurality of ligands, determining a relative strength of binding between the ligand and the protein to form a corresponding complex, wherein determining the relative strength comprises:\n calculating, using a computer, multiple relative binding free energy differences for a set of pairs of the ligand forming at least one closed thermodynamic cycle comprising a plurality of legs linking the ligand pairs; \n calculating, using the computer, a hysteresis magnitude associated with each closed thermodynamic cycle by a summation of the relative binding free energy differences for each of the ligand pairs that form a closed thermodynamic cycle, the hysteresis magnitude calculation comprising:\n a. determining, using a probabilistic model, the free energy differences and error distributions about those free energy differences along each of the legs of the closed thermodynamic cycle that probabilistically lead to the hysteresis magnitude observed for the closed thermodynamic cycles; \n b. determining a most probable free energy difference for each leg in the closed thermodynamic cycle included in the probabilistic model determined in step (a); \n c. determining a most probable error associated with the most probable binding free energy difference for each ligand pair along each leg in the closed thermodynamic cycle from the probabilistic determination in step (b); \n d. identifying which of the ligands form complexes with the protein based on the relative binding free energies and most probable errors determined in step (c); \n \n ranking the ligands identified as forming complexes with the protein based on the calculated relative binding free energies; identifying one or more of the ranked ligands as candidates for the drug based on the ranking; and experimentally evaluating at least one of the identified ranked ligands.

Metadata:
- Claim Count in Document: 35.0
- Percentile: 95.0
- Lexical Diversity: 1.68657
- Patent Class: 703.0
- Transitional Phrase Type: open
- Component Type: 1
- Foreign Priority: False
- Related Applications: ['10844258', '12791493', '12791448', '11982783', '11695494']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.2779430941908707
- 35 USC 102 Novelty (BERT): 0.505631873685735
- Combined Prediction Score: 0.3007119721403572
- Mean Citation Score: 214.15502200000003
- Max Citation Score: 241.59618
- Similarity Product: 162.07594428142906

Labels:
- Claim Label 101: 1
- Claim Label 102: 1
- Claim Label 103: 1
- Claim Label 112: 1
- Combined Label: 1
- Label 101 Adjusted: 1

Dataset: test