Matthew T Clark

US Patent:

20090094012, Apr 9, 2009

Filed:

Oct 9, 2007

Appl. No.:

11/869075

Inventors:

Matthew Clark - Wayne PA, US

Assignee:

LOCUS PHARMACEUTICALS, INC. - Blue Bell PA

International Classification:

G06G 7/48

US Classification:

703 11

Abstract:

Methods and systems for analyzing a macromolecule for potential binding sites are disclosed. Multiple molecular species and a free energy value may be selected. An operation for a molecular fragment of one of the molecular species may be selected from insertion, deletion and movement operations. The selected operation may be performed on a computer representation of an instance of a molecular fragment at one of a plurality of binding sites based on a grand canonical ensemble probability density function associated with the selected operation. Information may be stored pertaining to the plurality of binding sites. The operation selecting, performing and information storing operations may be performed multiple times. Multiple occupation probabilities may be provided based on the stored information. The occupation probabilities may include, for each molecular species, a probability that an instance of a molecular fragment of the molecular species resides at a binding site.

US Patent:

20090171642, Jul 2, 2009

Filed:

Dec 27, 2007

Appl. No.:

11/965139

Inventors:

George Talbot - Philadelphia PA, US
Matthew Clark - Wayne PA, US

Assignee:

LOCUS PHARMACEUTICALS, INC. - Blue Bell PA

International Classification:

G06G 7/48

US Classification:

703 12

Abstract:

Methods and systems for estimating the free energy of molecules from a plurality of fragments are disclosed. A number of poses for each fragment in an unbound state and a sum of the free energy values for each fragment may be determined. A number of acceptable poses for each of a plurality of fragments when bound may also be determined. An entropy loss may be estimated based on at least the number of acceptable poses for each of the plurality of fragments when bound and the number of poses for each fragment in an unbound state. A free energy value may be determined for the plurality of fragments when bound based on the entropy loss.

US Patent:

20110130968, Jun 2, 2011

Filed:

Nov 29, 2009

Appl. No.:

12/626911

Inventors:

Matthew Clark - Wayne PA, US

International Classification:

G06F 19/00
G01N 33/48

US Classification:

702 19

Abstract:

Methods and systems for computing the binding free energy of a ligand to a host are disclosed. The method entails selecting random poses of a ligand, including translation, rotation, and conformation, and computing the ligand-host interaction energy. The poses are accepted or rejected based on the Metropolis criteria. The entropies of interaction are estimated from the log of the ratio of accepted poses to attempted poses. The free energy of the entire sampling region, and of sub-regions of the binding region, can be accumulated by storing the energies and acceptance ratios for both the entire region and the sub regions. In order to better shape the protein to the ligand, energy minimization of the host atoms in the region of the ligand is carried out in the presence of the lowest free-energy pose of the ligand, optionally preceded by random perturbation of the Cartesian coordinates of the host atoms in the vicinity of the ligand.

US Patent:

20170346711, Nov 30, 2017

Filed:

May 27, 2016

Appl. No.:

15/167093

Inventors:

- Charlotte NC, US
Joseph Benjamin Castinado - North Glenn CO, US
Matthew Eugene Clark - Milpitas CA, US

International Classification:

H04L 12/26
H04W 4/02
H04L 12/927
H04W 24/02
G06Q 20/32

Abstract:

A system for monitoring resource utilization and optimization includes an entity system having a network communication interface and a memory device storing a resource monitoring and utilization application and a resource application. A processing device is operatively coupled to the memory device, wherein the processing device is configured to execute computer-readable program code to: determine based on the utilization of a resource application and/or a physical transaction related to the resource application to initiate the resource monitoring and utilization application; initiate the resource monitoring and utilization application to transmit information about the resource application to a user device.