Robert C Abel

US Patent:

7756674, Jul 13, 2010

Filed:

Nov 5, 2007

Appl. No.:

11/982783

Inventors:

Thomas Young - New York NY, US
Robert Abel - Davie FL, US
Richard A. Friesner - New York NY, US
Bruce J. Berne - Irvington NY, US

Assignee:

The Trustees of Columbia University in the City of New York - New York NY

International Classification:

G06F 17/18
G01N 33/53

US Classification:

702172, 702 19, 702 27, 702179

Abstract:

Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e. g. , “hydration sites”), computing the average system interaction energies of water molecules occupying the various hydrations sites, computing excess entropies of water molecules occupying the hydration sites; constructing a 3 dimensional hydration thermodynamics map of the protein active site; and computing relative binding affinities of congeneric ligands based on the principle that tighter binding ligands can displace more entropically structured and energetically depleted hydration sites from the active site into the bulk fluid.

US Patent:

7970580, Jun 28, 2011

Filed:

Jun 1, 2010

Appl. No.:

12/791448

Inventors:

Thomas Young - New York NY, US
Robert Abel - Davie FL, US
Richard A. Friesner - New York NY, US
Bruce J. Berne - Irvington NY, US

Assignee:

The Trustees of Columbia University in the City of New York - New York NY

International Classification:

G01N 33/48

US Classification:

702172, 702 19, 702 27, 702136, 374 45

Abstract:

Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e. g. , “hydration sites”), computing the average system interaction energies of water molecules occupying the various hydrations sites, computing excess entropies of water molecules occupying the hydration sites; constructing a 3 dimensional hydration thermodynamics map of the protein active site; and computing relative binding affinities of congeneric ligands based on the principle that tighter binding ligands can displace more entropically structured and energetically depleted hydration sites from the active site into the bulk fluid.

US Patent:

7970581, Jun 28, 2011

Filed:

Jun 1, 2010

Appl. No.:

12/791493

Inventors:

Thomas Young - New York NY, US
Robert Abel - Davie FL, US
Richard A. Friesner - New York NY, US
Bruce J. Berne - Irvington NY, US

Assignee:

The Trustees of Columbia University in the City of New York - New York NY

International Classification:

G01N 33/48

US Classification:

702172, 702 19, 702 27, 702136, 374 45

Abstract:

Described is a technique to exhaustively enumerate the thermodynamic properties of the water molecules solvating the active site of a protein in its apostate and calculate the relative binding affinities of congeneric compounds that bind to this protein. The subject matter includes sampling the configurations of the solvating water in the active site; extracting the thermodynamic information about the solvating water from these configurations by clustering the observed water configurations into regions of high water occupancy (e. g. , “hydration sites”), computing the average system interaction energies of water molecules occupying the various hydrations sites, computing excess entropies of water molecules occupying the hydration sites; constructing a 3 dimensional hydration thermodynamics map of the protein active site; and computing relative binding affinities of congeneric ligands based on the principle that tighter binding ligands can displace more entropically structured and energetically depleted hydration sites from the active site into the bulk fluid.

US Patent:

48100820, Mar 7, 1989

Filed:

Jul 1, 1987

Appl. No.:

7/068359

Inventors:

Robert Abel - Wilmington DE

International Classification:

G02C 704
A61F 214

US Classification:

351160R

Abstract:

A device for correcting refractive errors in the eye comprising a synthetic corneal onlay lens. The lens has an annular projection received in an annular recess in the corneal outer surface and a mechanism for connecting the lens to the cornea. This mechanism comprises sutures received in throughbores in the lens and passing into the cornea, adhesive directly connecting the annular projection and the recess, or both. The annular projection and the recess can have conforming scalloped surfaces to increase the engaging surface areas, thereby reducing the chances of relative rotation and increasing the adhesion therebetween.

US Patent:

46937153, Sep 15, 1987

Filed:

Jun 19, 1986

Appl. No.:

6/876177

Inventors:

Robert Abel - Wilmington DE

International Classification:

A61F 214

US Classification:

623 5

Abstract:

A corneal implant for replacing injured or opaque portions of a natural cornea. The implant comprises a substantially circular main body portion having anterior and posterior surfaces and a radially outwardly facing, substantially cylindrical peripheral surface. Means are provided on the main body portion for receiving sutures therethrough to securely couple the main body portion to the cornea. The peripheral surface has a height H greater than the thickness T of the corneal aperture so that when the corneal implant is sutured into place in a surgically created corneal aperture, the peripheral surface will extend posterior of the cornea to prevent the corneal membrane from growing over the posterior surface of the implant. The corneal implant can be easily attached by simple surgical techniques. First, the opaque or injured portions of the cornea are excised to provide a substantially circular corneal aperture.

US Patent:

20210035660, Feb 4, 2021

Filed:

Jul 15, 2020

Appl. No.:

16/929591

Inventors:

- New York NY, US
Yuqing Deng - New York NY, US
Yujie Wu - New York NY, US
Byungchan Kim - West New York NJ, US
Robert L. Abel - Brooklyn NY, US

International Classification:

G16C 20/50
G16B 15/00
G16B 15/30

Abstract:

A method for computing free energy difference between a reference molecule and a target molecule. The target molecule has the common set of atoms Pand a set of atoms P. The method includes applying a potential to restrain an interaction of the additional atomic component from the set of atoms Pwith the common set of atoms Pin the initial state. The method includes determining one or more transition states along a transformation path between the initial state and target state. The method includes scaling the restrain potential correspondingly along the transformation path until the potential becomes zero when a corresponding end state is reached, and calculating the free energy difference between the reference molecule and the target molecule using a value obtained along the transformation path from the initial state to the target state.

US Patent:

20190237165, Aug 1, 2019

Filed:

Feb 4, 2019

Appl. No.:

16/267085

Inventors:

- New York NY, US
Robert L. Abel - Brooklyn NY, US

International Classification:

G16C 20/30
G06F 17/50

Abstract:

Methods of calculating a free energy of solubility for a compound in a solvent by computer operations include the following steps: (i) establishing, using a computer model, an initial state for a system including an aggregate of multiple molecules of the compound in a solvent; (ii) establishing, using the computer model, a final state of the system including a single molecule from the aggregate fully solvated in the solvent and separate from a transformed aggregate; (iii) transforming, using the computer model, the system from the initial state to the final state, via removing a first molecule of the compound from the aggregate to form the transformed aggregate and replacing the first molecule with solvent at the site of the first molecule; and (iv) calculating the free energy of the transformation between the initial and the final states, which determines the free energy of solubility for the compound.

US Patent:

20190065697, Feb 28, 2019

Filed:

Aug 22, 2017

Appl. No.:

15/683678

Inventors:

- New York NY, US
Yuqing Deng - New York NY, US
Yujie Wu - New York NY, US
Byungchan Kim - West New York NJ, US
Robert Abel - Brooklyn NY, US

International Classification:

G06F 19/00
G06F 19/16

Abstract:

A method for computing free energy difference between a reference molecule and a target molecule. The target molecule has the common set of atoms Pand a set of atoms P. The method includes applying a potential to restrain an interaction of the additional atomic component from the set of atoms Pwith the common set of atoms Pin the initial state. The method includes determining one or more transition states along a transformation path between the initial state and target state. The method includes scaling the restrain potential correspondingly along the transformation path until the potential becomes zero when a corresponding end state is reached, and calculating the free energy difference between the reference molecule and the target molecule using a value obtained along the transformation path from the initial state to the target state.

Author:

Robert B. Abel

ISBN #:

0444015604

Author:

Robert B. Abel

ISBN #:

0761806989

Author:

Robert B. Abel

ISBN #:

0761806997

Author:

Robert Abel

ISBN #:

0671509314

Author:

Robert Abel

ISBN #:

0758202199

Author:

Robert Abel

ISBN #:

0758206224

Author:

Robert H. Abel

ISBN #:

0820312525