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: 20230360743Abstract: 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: ApplicationFiled: May 5, 2023Publication date: November 9, 2023Inventors: Peter Gedeck, Barry A. Bunin, William Michael Bowles, Philip Cheung, Alex Michael Clark
-
Publication number: 20220328141Abstract: 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: ApplicationFiled: March 31, 2022Publication date: October 13, 2022Applicant: Collaborative Drug Discovery, Inc.Inventors: Peter GEDECK, Barry A. BUNIN, Michael BOWLES, Philip CHEUNG, Alex Michael CLARK
-
Publication number: 20210287765Abstract: 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: ApplicationFiled: March 9, 2021Publication date: September 16, 2021Applicant: Collaborative Drug Discovery, Inc.Inventors: Barry A. BUNIN, Peter GEDECK
-
Patent number: 9594743Abstract: 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: GrantFiled: July 7, 2015Date of Patent: March 14, 2017Assignee: Collaborative Drug Discovery, Inc.Inventors: Barry A. Bunin, Nadia K. Litterman, Alex Clark
-
Publication number: 20160026622Abstract: 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: ApplicationFiled: July 7, 2015Publication date: January 28, 2016Inventors: Barry A. Bunin, Nadia K. Litterman, Alex Clark
-
Patent number: 8324174Abstract: 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: GrantFiled: December 22, 2011Date of Patent: December 4, 2012Assignee: Onyx Therapeutics, Inc.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Publication number: 20120277146Abstract: 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: ApplicationFiled: March 2, 2012Publication date: November 1, 2012Applicant: ONYX PHARMACEUTICALS INC.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Publication number: 20120101026Abstract: 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: ApplicationFiled: December 30, 2011Publication date: April 26, 2012Applicant: 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: 20120101050Abstract: 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: ApplicationFiled: December 22, 2011Publication date: April 26, 2012Applicant: Onyx Therapeutics, Inc.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Publication number: 20120101025Abstract: 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: ApplicationFiled: December 30, 2011Publication date: April 26, 2012Applicant: 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: 8129346Abstract: 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: GrantFiled: April 14, 2005Date of Patent: March 6, 2012Assignee: Onyx Therapeutics, Inc.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Patent number: 8088741Abstract: 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: GrantFiled: May 9, 2005Date of Patent: January 3, 2012Assignee: 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: 7491704Abstract: 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: GrantFiled: April 11, 2007Date of Patent: February 17, 2009Assignee: Proteolix, Inc.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Publication number: 20080200398Abstract: 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: ApplicationFiled: April 14, 2005Publication date: August 21, 2008Applicant: 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: 7232818Abstract: 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: GrantFiled: April 14, 2005Date of Patent: June 19, 2007Assignee: Proteolix, Inc.Inventors: Mark S. Smyth, Guy J. Laidig, Ronald T. Borchardt, Barry A. Bunin, Craig M. Crews, John H. Musser
-
Publication number: 20040147745Abstract: 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: ApplicationFiled: January 15, 2004Publication date: July 29, 2004Applicant: Axys Pharmaceuticals, Inc.Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
-
Publication number: 20030096796Abstract: 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: ApplicationFiled: July 24, 2002Publication date: May 22, 2003Applicant: AXYS PHARMACEUTICALS, INC.Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
-
Publication number: 20030087334Abstract: 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: ApplicationFiled: November 19, 2002Publication date: May 8, 2003Applicant: Libraria, Inc.Inventors: Barry A. Bunin, Timothy S. Powers, Guillermo Antonio Morales, Stephan C. Schurer, Steve M. Muskal, Oliver L. Saunders
-
Patent number: 6455502Abstract: 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: GrantFiled: March 15, 2000Date of Patent: September 24, 2002Assignee: AXYS Pharmaceuticals, Inc.Inventors: Clifford M. Bryant, Barry A. Bunin, Erica A. Kraynack, John W. Patterson
-
Publication number: 20020077757Abstract: 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: ApplicationFiled: November 28, 2001Publication date: June 20, 2002Applicant: Libraria, Inc.Inventors: Barry A. Bunin, Stephan C. Schurer, Steve M. Muskal