Patents Assigned to D. E. Shaw Research, LLC
  • Patent number: 11780845
    Abstract: The present disclosure relates to novel compounds and pharmaceutical compositions thereof, and methods for inhibiting the activity of FGFR enzymes with the compounds and compositions of the disclosure. The present disclosure further relates to, but is not limited to, methods for treating disorders associated with FGFR signaling with the compounds and compositions of the disclosure.
    Type: Grant
    Filed: January 31, 2023
    Date of Patent: October 10, 2023
    Assignees: Relay Therapeutics, Inc., D.E. Shaw Research, LLC
    Inventors: Bakary-Barry Touré, Heike Schoenherr, Fabrizio Giordanetto, Demetri T. Moustakas, Brandi M. Hudson
  • Patent number: 11701354
    Abstract: Cellular biological activities are tightly controlled by intracellular signaling processes initiated by extracellular signals. Protein tyrosine phosphatases, which remove phosphate groups from tyrosine phosphorylated signaling molecules, play equally important tyrosine roles as protein kinases in signal transduction. SHP-2, a cytoplasmic SH2 domain containing protein tyrosine phosphatase, is involved in the signaling pathways of a variety of growth factors and cytokines. Recent studies have clearly demonstrated that this phosphatase plays an important role in transducing signal relay from the cell surface to the nucleus, and is a critical intracellular regulator in mediating cell proliferation and differentiation.
    Type: Grant
    Filed: September 28, 2018
    Date of Patent: July 18, 2023
    Assignees: D. E. Shaw Research, LLC, Relay Therapeutics, Inc.
    Inventors: Alexander M. Taylor, W. Patrick Walters, Mark Andrew Murcko, Fabrizio Giordanetto, Eric Therrien, Sathesh Bhat, Markus Kristofer Dahlgren
  • Patent number: 11629145
    Abstract: The present invention relates to novel compounds and pharmaceutical compositions thereof, and methods for inhibiting the activity of SHP2 phosphatase with the compounds and compositions of the invention. The present invention further relates to, but is not limited to, methods for treating disorders associated with SHP2 deregulation with the compounds ad compositions of the invention.
    Type: Grant
    Filed: October 24, 2017
    Date of Patent: April 18, 2023
    Assignees: D. E. Shaw Research, LLC, Relay Therapeutics, Inc.
    Inventors: Fabrizio Giordanetto, Jack Benjamin Greisman, Paul Maragakis, Alexander M. Taylor, Lucian V. Dipietro, Elizabeth H. Kelley, André Lescarbeau, Mark Andrew Murcko, Levi Charles Thomas Pierce, Kelley C. Shortsleeves, W. Patrick Walters, Sathesh Bhat, Eric Therrien, Markus Kristofer Dahlgren
  • Patent number: 11591336
    Abstract: The present disclosure relates to compounds of formula (I) and pharmaceutical compositions thereof and methods for inhibiting the activity of SHP2 phosphatase with the compounds and compositions of the disclosure. The present disclosure further relates to, but is not limited to, methods for treating disorders associated with SHP2 deregulation with the compounds and compositions of the disclosure.
    Type: Grant
    Filed: May 25, 2018
    Date of Patent: February 28, 2023
    Assignees: D. E. Shaw Research, LLC, Relay Therapeutics, Inc.
    Inventors: Alexander M. Taylor, André Lescarbeau, Elizabeth H. Kelley, Kelley C. Shortsleeves, Lucian V. DiPietro, W. Patrick Walters, Mark Andrew Murcko, Levi Charles Thomas Pierce, Yong Tang, Fabrizio Giordanetto, Jack Benjamin Greisman, Paul Maragakis, Sathesh Bhat, Markus Kristofer Dahlgren, Eric Therrien
  • Publication number: 20230023559
    Abstract: A compound of Formula (I) or a pharmaceutically acceptable salt thereof is described, wherein the substituents are as defined herein. Pharmaceutical compositions comprising the same and method of using the same are also described.
    Type: Application
    Filed: October 6, 2020
    Publication date: January 26, 2023
    Applicants: D. E. Shaw Research, LLC, D. E. Shaw Research, LLC
    Inventors: Fabrizio GIORDANETTO, Morten Østergaard JENSEN, Vishwanath JOGINI, Roger John SNOW
  • Patent number: 11529348
    Abstract: Cellular biological activities are tightly controlled by intracellular signaling processes initiated by extracellular signals. Protein tyrosine phosphatases, which remove phosphate groups from tyrosine phosphorylated signaling molecules, play equally important tyrosine roles as protein kinases in signal transduction. SHP-2, a cytoplasmic SH2 domain containing protein tyrosine phosphatase, is involved in the signaling pathways of a variety of growth factors and cytokines. Recent studies have clearly demonstrated that this phosphatase plays an important role in transducing signal relay from the cell surface to the nucleus, and is a critical intracellular regulator in mediating cell proliferation and differentiation.
    Type: Grant
    Filed: September 28, 2018
    Date of Patent: December 20, 2022
    Assignees: D. E. Shaw Research, LLC, Relay Therapeutics, Inc.
    Inventors: Alexander M. Taylor, W. Patrick Walters, Mark Andrew Murcko, Fabrizio Giordanetto, Eric Therrien, Sathesh Bhat, Markus Kristofer Dahlgren
  • Patent number: 11529347
    Abstract: The present invention relates to novel compounds having the general formula: and pharmaceutical compositions thereof, and methods for inhibiting the activity of SHP2 phosphatase with the compounds and compositions of the invention. The present invention further relates to, but is not limited to, methods for suppressing tumor cell growth, ameliorating the pathogenesis of systemic lupus erythematosus, and the treatment of various other disorders, including Noonan syndrome, diabetes, neutropenia, neuroblastoma, melanoma, juvenile leukemia, juvenile myelomonocytic leukemia, chronic myelomonocytic leukemia, acute myeloid leukemia, and other cancers associated with SHP2 deregulation with the compounds and compositions of the invention, alone or in combination with other treatments.
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: December 20, 2022
    Assignees: Relay Therapeutics, Inc., D. E. Shaw Research, LLC
    Inventors: Brian K. Albrecht, Fabrizio Giordanetto, Jack Benjamin Greisman, Paul Maragakis, Alexander M. Taylor, W. Patrick Walters
  • Patent number: 11264120
    Abstract: A method for managing flow of particles into an array of pairwise-point-interaction-module includes receiving a first set of particles into a first queue. The first set is a proper subset of a second set of particles that comprises all particles that are to be passed into an array of pairwise-point-interaction-modules during a current time period. Prior to having received all particles from the second set, particles from the first set are allowed to pass from the first queue into the array.
    Type: Grant
    Filed: September 10, 2019
    Date of Patent: March 1, 2022
    Assignee: D. E. Shaw Research, LLC
    Inventors: Ping Tak Peter Tang, J. P. Grossman, Brannon Batson, Ron Dror
  • Patent number: 11139049
    Abstract: A method comprising causing a simulation machine for molecular dynamic simulation to determine that a topological distance that separates two particles is less than a threshold. The simulation machine includes nodes connected by a network. The nodes collectively representing a volume with each node corresponding to a portion of the simulation space. A topological relationship between the nodes corresponds to spatial relationship thereof in the simulation space. The simulation volume is occupied by particles that interact with each other. The two particles are among these particles. The simulation volume includes node boxes, each of which is handled by one of the nodes. Each of the nodes is implemented as an application specific integrated circuit that includes a combination of first and second hardware elements. The first hardware elements are especially designed to perform pairwise interactions. The second hardware elements operate to provide potentially interacting particles to the first hardware elements.
    Type: Grant
    Filed: November 16, 2015
    Date of Patent: October 5, 2021
    Assignee: D.E. Shaw Research, LLC
    Inventors: Ping Tak Peter Tang, J. P. Grossman, Brannon Batson, Ron Dror
  • Publication number: 20200375996
    Abstract: A method for treating neurodegenerative disease in a subject in need thereof by administering to the subject an effective amount of a Nedd4 activator as described herein.
    Type: Application
    Filed: December 14, 2016
    Publication date: December 3, 2020
    Applicants: D.E. Shaw Research, LLC, WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH
    Inventors: Yibing SHAN, Venkat MYSORE, Susan LINDQUIST, Dan TARDIFF, Srividya CHANDRAMOULI
  • Patent number: 10824422
    Abstract: A method for performing computations associated with bodies located in a computation region includes, for each subset of multiple subsets of the computations, performing the computations in that subset of computations, including accepting data of bodies located in each of a plurality of import regions associated with the subset of the computations, the import regions being parts of the computation region; for each combination of a predetermined plurality of combinations of multiple of the import regions, performing computations associated with sets of bodies, wherein for each of the sets of bodies, at least one body of the set is located in each import region of the combination.
    Type: Grant
    Filed: December 19, 2011
    Date of Patent: November 3, 2020
    Assignee: D.E. Shaw Research, LLC
    Inventors: Kevin J. Bowers, Ron Dror, David Shaw
  • Patent number: 10753947
    Abstract: In one aspect, the invention relates to a method for identifying a compound which modulates the activity of a voltage-gated protein. In certain embodiments, the voltage gate protein is a voltage-gated ion channel. In certain embodiments, the voltage-gated protein is a voltage sensitive phosphatase. In certain embodiments, the voltage-gated protein used in conjunction with the methods of the invention is modified to altered permeability or voltage sensitivity.
    Type: Grant
    Filed: August 29, 2014
    Date of Patent: August 25, 2020
    Assignee: D.E. SHAW RESEARCH, LLC
    Inventors: Morten Østergaard Jensen, David Wayne Borhani, Vishwanath Jogini
  • Patent number: 10739354
    Abstract: In one aspect, the invention relates to a method for identifying a compound which modulates the activity of a voltage-gated protein. In certain embodiments, the voltage gate protein is a voltage-gated ion channel. In certain embodiments, the voltage-gated protein is a voltage sensitive phosphatase. In certain embodiments, the voltage-gated protein used in conjunction with the methods of the invention is modified to altered permeability or voltage sensitivity.
    Type: Grant
    Filed: October 17, 2016
    Date of Patent: August 11, 2020
    Assignee: D.E. SHAW RESEARCH, LLC
    Inventors: Morten Østergaard Jensen, David Wayne Borhani, Vishwanath Jogini
  • Patent number: 9906467
    Abstract: A data communication apparatus includes a router, first and second packet producers, and a penalizer. The router is directly connected to the first and second producers. The penalizer assesses penalties against each producer whenever that producer is serviced. The penalty value depends at least in part on an expected extent to which the first producer requires service. The penalizer then accumulates penalties against each producer.
    Type: Grant
    Filed: June 15, 2015
    Date of Patent: February 27, 2018
    Assignee: D.E. Shaw Research, LLC
    Inventors: J. P. Grossman, Brian Patrick Towles
  • Patent number: 9747099
    Abstract: A computation system for computing interactions in a multiple-body simulation includes an array of processing modules arranged into one or more serially interconnected processing groups of the processing modules. Each of the processing modules includes storage for data elements and includes circuitry for performing pairwise computations between data elements each associated with a spatial location. Each of the pairwise computations makes use of a data element from the storage of the processing module and a data element passing through the serially interconnected processing modules. Each of the processing modules includes circuitry for selecting the pairs of data elements according to separations between spatial locations associated with the data elements.
    Type: Grant
    Filed: November 19, 2012
    Date of Patent: August 29, 2017
    Assignee: D.E. Shaw Research LLC
    Inventors: David E. Shaw, Martin M. Deneroff, Ron O. Dror, Richard H. Larson, John K. Salmon
  • Patent number: 9612832
    Abstract: A parallel processing system for computing particle interactions includes a plurality of computation nodes arranged according to a geometric partitioning of a simulation volume. Each computation node has storage for particle data. This particle data is associated with particles in a region of the geometrically partitioned simulation volume. The parallel processing system also includes a communication system having links interconnecting the computation nodes. Each of the computation nodes includes a processor subsystem. These processor subsystems cooperate to coordinate computation of the particle interactions in a distributed manner.
    Type: Grant
    Filed: February 1, 2013
    Date of Patent: April 4, 2017
    Assignee: D.E. Shaw Research LLC
    Inventors: David E. Shaw, Martin M. Deneroff, Ron O. Dror, Richard H. Larson, John K. Salmon
  • Patent number: 9384047
    Abstract: An apparatus for high-performance parallel computation, includes plural computation nodes, each having dispatch units, memories in communication with the dispatch units, and processors, each of which is in communication with the memories and the dispatch units. Each dispatch unit is configured to recognize, as ready for execution, one or more computational tasks that have become ready for execution as a result of counted remote writes into the memories. Each of the dispatch units is configured to receive a dispatch request from a processor and to determine whether there exist one or more computational tasks that are both ready and available for execution by the processor.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: July 5, 2016
    Assignee: D.E. Shaw Research, LLC
    Inventors: J. P. Grossman, Jeffrey S. Kuskin
  • Patent number: 9031241
    Abstract: An approach to data communication makes use of a protocol for encoding data on a serial link that provides both a run length limiting function and a frame marking function, while minimizing communication overhead over the data bearing portions of the signal, and while limiting latency introduced into the communication. In some examples, a single bit is added as a frame marker in such a way that a single bit frame marker also limits run length.
    Type: Grant
    Filed: February 4, 2010
    Date of Patent: May 12, 2015
    Assignee: D.E. Shaw Research, LLC
    Inventors: Larry Nociolo, Brian Patrick Towles
  • Patent number: 8918305
    Abstract: Distributed computation of multiple body interactions in a region uses multiple processing modules, where each of the processing modules is associated with a respective corresponding portion of the region. In some examples, the approach includes establishing multiple coordinate frames of reference, each processing module corresponding to one the coordinate frames of reference. In some examples, efficient techniques are used for selecting elements for computation of interactions according at least in part to a separation-based criterion.
    Type: Grant
    Filed: March 21, 2008
    Date of Patent: December 23, 2014
    Assignee: D.E. Shaw Research, LLC
    Inventor: Kevin J. Bowers
  • Patent number: 8473966
    Abstract: An inter-processor communication approach is applicable to a message passing pattern called iterative exchange. In such patterns, two processors exchange messages, then perform a computation, and then this process is repeated. If two sets of send and receive buffers are used, then it is possible to guarantee that a receive buffer on the receiver's side is always available to receive the message. A message passing system controls which buffers are used for sending and receiving. These buffers are registered beforehand, thereby avoiding repeated registration at the time messages are sent. The sender is initially informed of all the possible receive buffers that the receiver will use, and the sender then uses these receive buffers alternately. Examples of this approach can avoid the use of multiple-step rendezvous protocols, memory copies, and memory registrations when a message needs to be sent.
    Type: Grant
    Filed: October 1, 2007
    Date of Patent: June 25, 2013
    Assignee: D.E. Shaw Research, LLC
    Inventor: Edmond Chow