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8 research outcomes, page 1 of 1
  • publication . Preprint . Article . Other literature type . 2018
    Open Access
    Authors:
    Nguyen, Trung Hai; Rustenburg, Ariën S.; Krimmer, Stefan G.; Zhang, Hexi; Clark, John D.; Novick, Paul A.; Branson, Kim; Pande, Vijay S.; Chodera, John D.; Minh, David D. L.;
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | The role of reorganizatio... (5R01GM121505-02), NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Sound-stage Virtual Scree... (1R15GM114781-01A1)

    <jats:title>Abstract</jats:title><jats:p>Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, howe...

  • publication . Article . Other literature type . Preprint . 2018
    Open Access English
    Authors:
    Josh Fass; David A. Sivak; Gavin E. Crooks; Kyle A. Beauchamp; Benedict Leimkuhler; John D. Chodera;
    Project: NSERC , NIH | The role of reorganizatio... (5R01GM121505-02), NIH | MOUSE GENETICS (2P30CA008748-43), RCUK | Data-Driven Coarse-Graini... (EP/P006175/1), NSF | D3SC: EAGER: Collaborativ... (1738979)

    <jats:title>Abstract</jats:title><jats:p>While Langevin integrators are popular in the study of equilibrium properties of complex systems, it is challenging to estimate the timestep-induced discretization error: the degree to which the sampled phase-space or configurati...

  • publication . Preprint . 2018
    Open Access
    Authors:
    Swenson, David W.H.; Prinz, Jan-Hendrik; Noe, Frank; Chodera, John D.; Bolhuis, Peter G.;
    Publisher: Cold Spring Harbor Laboratory
    Project: EC | ScaleCell (772230), EC | E-CAM (676531), NIH | The role of reorganizatio... (5R01GM121505-02), NIH | MOUSE GENETICS (2P30CA008748-43)

    <jats:p>The OpenPathSampling (OPS) package provides an easy-to-use framework to apply transition path sampling methodologies to complex molecular systems with a minimum of effort. Yet, the extensibility of OPS allows for the exploration of new path sampling algorithms b...

  • publication . Preprint . 2018
    Open Access
    Authors:
    Chen, Shi; Wiewiora, Rafal P.; Meng, Fanwang; Babault, Nicolas; Ma, Anqi; Yu, Wenyu; Qian, Kun; Hu, Hao; Zou, Hua; Wang, Junyi; ...
    Publisher: Cold Spring Harbor Laboratory
    Project: NSERC , NIH | Discovery of Selective In... (5R01GM122749-02), NIH | MOUSE GENETICS (2P30CA008748-43), NIH | Mechanism and Inhibition ... (5R01GM126154-02), NIH | The role of reorganizatio... (5R01GM121505-02), EC | ULTRA-DD (115766), WT , NIH | Targeting Lysine Methyltr... (5R01CA218600-02), NIH | Epigenetic Therapy and Pr... (5R01HD088626-02), NIH | Profile substrates and in... (1R01GM096056-01)

    <jats:title>Abstract</jats:title><jats:p>Elucidating conformational heterogeneity of proteins is essential for understanding protein functions and developing exogenous ligands for chemical perturbation. While structural biology methods can provide atomic details of stat...

  • publication . Preprint . 2018
    Open Access
    Authors:
    Swenson, David W.H.; Prinz, Jan-Hendrik; Noe, Frank; Chodera, John D.; Bolhuis, Peter G.;
    Publisher: Cold Spring Harbor Laboratory
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | The role of reorganizatio... (5R01GM121505-02), EC | ScaleCell (772230), EC | E-CAM (676531)

    <jats:p>Transition path sampling techniques allow molecular dynamics simulations of complex systems to focuson rare <jats:italic>dynamical events</jats:italic>, providing insight into mechanisms and the ability to calculate rates inaccessibleby ordinary dynamics simulat...

  • publication . Article . Other literature type . 2019
    Open Access English
    Authors:
    Shi Chen; Rafal P Wiewiora; Fanwang Meng; Nicolas Babault; Anqi Ma; Wenyu Yu; Kun Qian; Hao Hu; Hua Zou; Junyi Wang; ...
    Publisher: eLife Sciences Publications, Ltd
    Project: NIH | Mechanism and Inhibition ... (5R01GM126154-02), NIH | The role of reorganizatio... (5R01GM121505-02), NIH | MOUSE GENETICS (2P30CA008748-43), NSERC , EC | ULTRA-DD (115766), NIH | Discovery of Selective In... (5R01GM122749-02), NIH | Profile substrates and in... (1R01GM096056-01), WT , NIH | Interrogating Functions o... (1R01GM120570-01)

    Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illu...

  • publication . Article . Other literature type . Preprint . 2017
    Open Access
    Authors:
    Hauser, Kevin; Negron, Christopher; Albanese, Steven K.; Ray, Soumya; Steinbrecher, Thomas; Abel, Robert; Chodera, John D.; Wang, Lingle;
    Publisher: Springer Science and Business Media LLC
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | The role of reorganizatio... (5R01GM121505-02)

    The therapeutic effect of targeted kinase inhibitors can be significantly reduced by intrinsic or acquired resistance mutations that modulate the affinity of the drug for the kinase. In cancer, the majority of missense mutations are rare, making it difficult to predict ...

  • publication . Other literature type . Conference object . 2019
    Open Access English
    Authors:
    Wang, Yuanqing;
    Publisher: Zenodo
    Project: NIH | MOUSE GENETICS (2P30CA008748-43), NIH | The role of reorganizatio... (5R01GM121505-02), NSF | D3SC: EAGER: Collaborativ... (1738979)

    <p>Yuanqing Wang (MSKCC) gave a talk about using Graph Nets for fast prediction of atomic partial charges as a part of OFF webinar series. The preprint is available <a href="https://arxiv.org/abs/1909.07903">here</a>.</p> <p><br> <strong>Abstract:</strong> Here we show ...

8 research outcomes, page 1 of 1
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