Patents by Inventor Barry A. Bunin

Barry A. Bunin has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20230360743
    Abstract: A method includes converting, by a generative network, an input into a latent vector representation of a sample chemical compound, wherein the input is one of an order-dependent representation of the sample chemical compound and a molecular graph representation of the sample chemical compound; determining, by an output neural network, one or more properties of the sample chemical compound based on the latent vector representation of the sample chemical compound; performing, by the output neural network, an optimization routine to select a candidate latent vector representation from among a plurality of latent vector representations based on the latent vector representation of the sample chemical compound, wherein the plurality of latent vector representations includes the latent vector representation of the sample chemical compound; and identifying, by the output neural network, a candidate chemical compound based on the candidate latent vector representation.
    Type: Application
    Filed: May 5, 2023
    Publication date: November 9, 2023
    Inventors: Peter Gedeck, Barry A. Bunin, William Michael Bowles, Philip Cheung, Alex Michael Clark
  • Publication number: 20220328141
    Abstract: A method includes generating a graph of a chemical compound based on at least one of an order-dependent representation of the chemical compound and a molecular graph representation of the chemical compound, encoding the graph based on an adjacency matrix of a graph convolutional neural network (GCN), an activation function of the GCN, and one or more weights of the GCN to generate a latent vector representation of the chemical compound, and decoding the latent vector representation based on a plurality of hidden states of a neural network (NN) to generate a reproduced order-dependent representation of the chemical compound.
    Type: Application
    Filed: March 31, 2022
    Publication date: October 13, 2022
    Applicant: Collaborative Drug Discovery, Inc.
    Inventors: Peter GEDECK, Barry A. BUNIN, Michael BOWLES, Philip CHEUNG, Alex Michael CLARK
  • Publication number: 20210287765
    Abstract: A method includes identifying, using one or more processors, a first plurality of fragments of a first structure graph representing a first chemical compound, and generating, using the one or more processors, a first plurality of subgraphs of the first structure graph based on the first plurality of fragments. The method includes generating, using the one or more processors, a first plurality of nodes based on the first plurality of subgraphs. The method includes arranging, using the one or more processors, the first plurality of nodes based on a number of the first plurality of fragments associated with each of the first plurality of subgraphs. The method includes connecting, using the one or more processors, the first plurality of nodes using a first plurality of edges and based on one or more reduced graph rules.
    Type: Application
    Filed: March 9, 2021
    Publication date: September 16, 2021
    Applicant: Collaborative Drug Discovery, Inc.
    Inventors: Barry A. BUNIN, Peter GEDECK
  • Patent number: 9594743
    Abstract: A process for identifying, accurately selecting, and storing scientific data that is present in textual formats. The process includes providing scientific data located in a text document and searching the text document using a computer and selecting a plurality of key words and phrases using an algorithm. The selected key words and phrases are matched with a plurality of semantic definitions and a plurality of semantic definition-key words and phrase pairs are created. The created plurality of semantic definition-key words and phrase pairs are displayed to a user via a computer user interface and the user selects which of the created plurality of semantic definition-key words and phrase pairs are accurate. The process also includes storing the selected and accurate semantic definition-key words and phrase pairs in computer memory.
    Type: Grant
    Filed: July 7, 2015
    Date of Patent: March 14, 2017
    Assignee: Collaborative Drug Discovery, Inc.
    Inventors: Barry A. Bunin, Nadia K. Litterman, Alex Clark
  • Publication number: 20160026622
    Abstract: A process for identifying, accurately selecting, and storing scientific data that is present in textual formats. The process includes providing scientific data located in a text document and searching the text document using a computer and selecting a plurality of key words and phrases using an algorithm. The selected key words and phrases are matched with a plurality of semantic definitions and a plurality of semantic definition-key words and phrase pairs are created. The created plurality of semantic definition-key words and phrase pairs are displayed to a user via a computer user interface and the user selects which of the created plurality of semantic definition-key words and phrase pairs are accurate. The process also includes storing the selected and accurate semantic definition-key words and phrase pairs in computer memory.
    Type: Application
    Filed: July 7, 2015
    Publication date: January 28, 2016
    Inventors: Barry A. Bunin, Nadia K. Litterman, Alex Clark
  • Patent number: 8324174
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Grant
    Filed: December 22, 2011
    Date of Patent: December 4, 2012
    Assignee: Onyx Therapeutics, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Publication number: 20120277146
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Application
    Filed: March 2, 2012
    Publication date: November 1, 2012
    Applicant: ONYX PHARMACEUTICALS INC.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Publication number: 20120101026
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Application
    Filed: December 30, 2011
    Publication date: April 26, 2012
    Applicant: ONYX THERAPEUTICS, INC.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser, Kevin D. Shenk, Peggy A. Radel
  • Publication number: 20120101050
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Application
    Filed: December 22, 2011
    Publication date: April 26, 2012
    Applicant: Onyx Therapeutics, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Publication number: 20120101025
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Application
    Filed: December 30, 2011
    Publication date: April 26, 2012
    Applicant: ONYX THERAPEUTICS, INC.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser, Kevin D. Shenk, Peggy A. Radel
  • Patent number: 8129346
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Grant
    Filed: April 14, 2005
    Date of Patent: March 6, 2012
    Assignee: Onyx Therapeutics, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Patent number: 8088741
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsinlike activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Grant
    Filed: May 9, 2005
    Date of Patent: January 3, 2012
    Assignee: Onyx Therapeutics, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser, Kevin D. Shenk, Peggy A. Radel
  • Patent number: 7491704
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Grant
    Filed: April 11, 2007
    Date of Patent: February 17, 2009
    Assignee: Proteolix, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Publication number: 20080200398
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Application
    Filed: April 14, 2005
    Publication date: August 21, 2008
    Applicant: Proteolix, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser, John S. Schneekloth Jr, John Clifford Chabala
  • Patent number: 7232818
    Abstract: Peptide-based compounds including heteroatom-containing, three-membered rings efficiently and selectively inhibit specific activities of N-terminal nucleophile (Ntn) hydrolases. The activities of those Ntn having multiple activities can be differentially inhibited by the compounds described. For example, the chymotrypsin-like activity of the 20S proteasome may be selectively inhibited with the inventive compounds. The peptide-based compounds include at least three peptide units, an epoxide or aziridine, and functionalization at the N-terminus. Among other therapeutic utilities, the peptide-based compounds are expected to display anti-inflammatory properties and inhibition of cell proliferation.
    Type: Grant
    Filed: April 14, 2005
    Date of Patent: June 19, 2007
    Assignee: Proteolix, Inc.
    Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
  • Publication number: 20040147745
    Abstract: The present invention relates to novel N-cyanomethyl amides which are cysteine protease inhibitors, the pharmaceutically acceptable salts and N-oxides thereof, their uses as therapeutic agents and the methods of their making.
    Type: Application
    Filed: January 15, 2004
    Publication date: July 29, 2004
    Applicant: Axys Pharmaceuticals, Inc.
    Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
  • Publication number: 20030096796
    Abstract: The present invention relates to novel N-cyanomethyl amides which are cysteine protease inhibitors, the pharmaceutically acceptable salts and N-oxides thereof, their uses as therapeutic agents and the methods of their making.
    Type: Application
    Filed: July 24, 2002
    Publication date: May 22, 2003
    Applicant: AXYS PHARMACEUTICALS, INC.
    Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
  • Publication number: 20030087334
    Abstract: Computational tools automatically suggest/generate diverse reaction sets for particular precursors, classes of precursors, or different reaction chemistries. This is accomplished by automatically generating a group of reaction chemistries for a particular precursor or class of precursors. Some of the reactions and/or products may be produced without reliance on reactions and products reported in available references.
    Type: Application
    Filed: November 19, 2002
    Publication date: May 8, 2003
    Applicant: Libraria, Inc.
    Inventors: Barry A. Bunin, Timothy S. Powers, Guillermo Antonio Morales, Stephan C. Schurer, Steve M. Muskal, Oliver L. Saunders
  • Patent number: 6455502
    Abstract: The present invention relates to novel N-cyanomethyl amides which are cysteine protease inhibitors, the pharmaceutically acceptable salts and N-oxides thereof, their uses as therapeutic agents and the methods of their making.
    Type: Grant
    Filed: March 15, 2000
    Date of Patent: September 24, 2002
    Assignee: AXYS Pharmaceuticals, Inc.
    Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
  • Publication number: 20020077757
    Abstract: Reaction steps are organized as belonging to particular reaction protocols within a database. Each reaction may represent a discrete step in a multi-step protocol for making a final product from a starting reactant. To populate the database, a system receives information separately from a plurality of references (e.g., literature articles, patent publications, etc.). Such information typically includes descriptions of reaction steps presented in the references (e.g., detailed recipes for performing the reaction steps). Alternatively, or in addition, the methodology includes identifying at least one protocol specified in the reference, which protocol comprises two or more reaction steps, and then specifying that the two or more reaction steps belong to the protocol.
    Type: Application
    Filed: November 28, 2001
    Publication date: June 20, 2002
    Applicant: Libraria, Inc.
    Inventors: Barry A. Bunin, Stephan C. Schurer, Steve M. Muskal