公开(公告)号：US20220108766A1

公开(公告)日：2022-04-07

申请号：US17420582

申请日：2020-01-02

申请人： CYCLICA INC.

发明人： Stephen Scott Mackinnon ,  Zhaleh Safikhani ,  Robert Vernon ,  Andrew E. Brereton ,  Andreas Windemuth

IPC分类号： G16B15/30 ,  G16B40/20

摘要： A method for predicting drug-target binding using synthetically-augmented data involves generating a multitude of ghost ligands for a multitude of proteins in a protein structure database, generating a multitude of drug-target interaction (DTI) features for proteins and ligands in a DTI database, using the multitude of ghost ligands, generating a machine learning model using the multitude of DTI features, and predicting a likelihood of interaction for a combination of a query protein and a query ligand using the machine learning model.

公开(公告)号：US20190018924A1

公开(公告)日：2019-01-17

申请号：US16067465

申请日：2015-12-31

申请人： Cyclica Inc.

发明人： Stephen Scott Mackinnon ,  Leonard David Morayniss ,  Jason Mitakidis ,  Fuad G. Gwadry

IPC分类号： G06F19/18 ,  G06F19/12 ,  G06F19/16 ,  G06F19/28

摘要： The invention involves a method for identifying a target protein. The invention involves receiving a request to identify a target protein based on a ligand; identifying, using the ligand, a first protein, where the ligand binds with the first protein to form a ligand-protein complex; generating, a first binding site profile for the first protein, where the first binding site profile describes molecular properties of the first protein; obtaining, from a controlled server, structure data describing molecular properties of surfaces for a multitude of proteins, where the multitude of proteins comprises the target protein; identifying, using the first binding site profile and the structure data, the target protein; and presenting the target protein to a user.

公开(公告)号：US12033723B2

公开(公告)日：2024-07-09

申请号：US16067465

申请日：2015-12-31

申请人： Cyclica Inc.

发明人： Stephen Scott Mackinnon ,  Leonard David Morayniss ,  Jason Mitakidis ,  Fuad G. Gwadry

IPC分类号： G16B20/30 ,  G16B5/00 ,  G16B15/00 ,  G16B15/30 ,  G16B20/00 ,  G16B35/00 ,  G16B35/20 ,  G16B50/00 ,  G16B50/10 ,  G16B50/30 ,  G16B99/00 ,  G16C20/60

CPC分类号： G16B20/30 ,  G16B5/00 ,  G16B15/00 ,  G16B15/30 ,  G16B20/00 ,  G16B35/00 ,  G16B35/20 ,  G16B50/00 ,  G16B50/10 ,  G16B50/30 ,  G16B99/00 ,  G16C20/60

摘要： The invention involves a method for identifying a target protein. The invention involves receiving a request to identify a target protein based on a ligand; identifying, using the ligand, a first protein, where the ligand binds with the first protein to form a ligand-protein complex; generating, a first binding site profile for the first protein, where the first binding site profile describes molecular properties of the first protein; obtaining, from a controlled server, structure data describing molecular properties of surfaces for a multitude of proteins, where the multitude of proteins comprises the target protein; identifying, using the first binding site profile and the structure data, the target protein; and presenting the target protein to a user.

公开(公告)号：US20240321391A1

公开(公告)日：2024-09-26

申请号：US18734587

申请日：2024-06-05

申请人： Cyclica Inc.

发明人： Stephen Scott MACKINNON ,  Leonard David MORAYNISS ,  Jason MITAKIDIS ,  Fuad G GWADRY

IPC分类号： G16B20/30 ,  G16B5/00 ,  G16B15/00 ,  G16B15/30 ,  G16B20/00 ,  G16B35/00 ,  G16B35/20 ,  G16B50/00 ,  G16B50/10 ,  G16B50/30 ,  G16B99/00 ,  G16C20/60

CPC分类号： G16B20/30 ,  G16B5/00 ,  G16B15/00 ,  G16B15/30 ,  G16B20/00 ,  G16B35/00 ,  G16B35/20 ,  G16B50/00 ,  G16B50/10 ,  G16B50/30 ,  G16B99/00 ,  G16C20/60

摘要： The invention involves a method for identifying a target protein. The invention involves receiving a request to identify a target protein based on a ligand; identifying, using the ligand, a first protein, where the ligand binds with the first protein to fonn a ligand-protein complex; generating, a first binding site profile for the first protein, where the first binding site profile describes molecular properties of the first protein; obtaining, from a controlled server, structure data describing molecular properties of surfaces for a multitude of proteins, where the multitude of proteins comprises the target protein; identifying, using the first binding site profile and the structure data, the target protein; and presenting the target protein to a user.

公开(公告)号：US12087409B2

公开(公告)日：2024-09-10

申请号：US17276093

申请日：2019-09-13

申请人： CYCLICA INC.

发明人： Andrew Edward Brereton ,  Sana Alwash ,  Stephen Scott Mackinnon ,  Joseph Christian Campbell Somody ,  Andreas Windemuth

IPC分类号： G16C20/30

CPC分类号： G16C20/30

摘要： A method for predicting a property of a sample molecule involves, for each of a multitude of reference molecules, obtaining a multitude of fingerprints and at least one property, and obtaining the multitude of fingerprints of the sample molecule. The method further involves for each of the multitude of reference molecules, using each of the multitude of fingerprints, calculating distances to the sample molecule, and for each of the multitude of reference molecules, determining a relative predictive dominance, based on the distances to the sample molecule. The method also involves, for each of the multitude of reference molecules, determining a fitness value based on the relative predictive dominance, and predicting the at least one property of the sample molecule based on the at least one property of the multitude of reference molecules and the fitness values obtained for the reference molecules.