US 12,224,040 B2
Movable type method applied to protein-ligand binding
Zheng Zheng, Gainesville, FL (US); and Kenneth M. Merz, Jr., Ann Arbor, MI (US)
Assigned to Board of Trustees of Michigan State University, East Lansing, MI (US); and University of Florida Research Foundation, Inc., Gainesville, FL (US)
Filed by Board of Trustees of Michigan State University, East Lansing, MI (US); and University of Florida Research Foundation, Inc., Gainesville, FL (US)
Filed on Apr. 16, 2019, as Appl. No. 16/385,735.
Application 16/385,735 is a division of application No. 15/143,519, filed on Apr. 30, 2016, granted, now 10,332,616.
Application 15/143,519 is a continuation in part of application No. PCT/US2014/063328, filed on Oct. 31, 2014.
Claims priority of provisional application 61/898,718, filed on Nov. 1, 2013.
Prior Publication US 2019/0378592 A1, Dec. 12, 2019
Int. Cl. C40B 30/04 (2006.01); G01N 33/68 (2006.01); G06F 17/18 (2006.01); G16B 5/00 (2019.01); G16B 5/20 (2019.01); G16B 15/00 (2019.01); G16B 15/20 (2019.01); G16B 15/30 (2019.01); G16C 20/50 (2019.01); G16C 20/90 (2019.01)
CPC G16B 15/30 (2019.02) [C40B 30/04 (2013.01); G01N 33/68 (2013.01); G06F 17/18 (2013.01); G16B 5/00 (2019.02); G16B 5/20 (2019.02); G16B 15/00 (2019.02); G16B 15/20 (2019.02); G16C 20/50 (2019.02); G16C 20/90 (2019.02)] 15 Claims
 
1. A method of estimating a pose of a ligand in a protein receptor comprising:
identifying all possible atom pairs of protein receptor-ligand complexes in a given configuration space for a system that comprises proteins;
creating a first database and a second database; where the first database comprises associated pairwise distant dependent energies and where the second database comprises all probabilities, interaction energy parameters, and/or distances that include how the atom pairs can combine;
combining the first database with the second database via statistical mechanics to accurately estimate binding free energies as well as the pose of the ligand in the protein receptor; and
selecting a protein receptor-ligand complex for further study.