Applications > desmond

Publications

Users of this package associated the following 12 publications with the XSEDE allocation/account under which they were running this software. Thus the publications may have come before or after the runs of this software, but the authors considered them to be related to the same line of research.

  • S. Wan, David Wright (University College, London), P. V. Coveney, (August2012) "Mechanism of Drug Efficacy within the Epidermal Growth Factor Receptor Revealed by Microsecond Molecular Dynamics Simulation", Molecular Cancer Therapeutics undefined / undefined, . http://dx.doi.org/10.1158/1535-7163.MCT-12-0644-T
  • Mauro Lapelosa, Emilio Gallicchio, Ronald Levy (Rutgers, the State University of New Jersey), (2012) "Conformational transitions and convergence of absolute binding free energy calculations.", Journal of Chemical Theory and Computation , .
  • Emilio Gallicchio, Ronald Levy (Rutgers, the State University of New Jersey), (2012) "Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).", Journal of Computer-Aided Molecular Design , .
  • Sara Nichols (University of California-San Diego), Carlos Hernandez (Stanford University), Yi Wang (University of California-San Diego), James McCammon (University of California-San Diego), (June2013) "Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface", Protein Science 22 / 6, 745-754. http://dx.doi.org/10.1002/pro.2258
  • David Wright (University College, London), S. Kashif Sadiq, Gianni De Fabritiis, Peter V. Coveney, (July2012) "Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase", Journal of the American Chemical Society 134 / 31, 12885-12888. http://dx.doi.org/10.1021/ja301565k
  • David Wright (University College, London), Benjamin A. Hall, Paul Kellam, Peter V. Coveney, (June2012) "Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors", Biology 1 / 2, 222-244. http://dx.doi.org/10.3390/biology1020222
  • Emilio Gallicchio (City University of New York), Nanjie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy, (2014) "Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge", Journal of Computer-Aided Molecular Design undefined / undefined, . http://dx.doi.org/10.1007/s10822-014-9711-9
  • Lauren Wickstrom, Peng He, Emilio Gallicchio, Ronald Levy (Rutgers, the State University of New Jersey), (2013) "Large scale affinity calculations of cyclodextrin host-guest complexes: understanding the role of reorganization in the molecular recognition process.", Journal of Chemical Theory and Computation , .
  • Zhiqiang Tan, Emilio Gallicchio, Mauro Lapelosa, Ronald Levy (Rutgers, the State University of New Jersey), (2012) "Theory of binless multi-state free energy estimation with applications to protein-ligand binding.", The Journal of Chemical Physics , .
  • Luca Larini (University of California-Santa Barbara), Lanyuan Lu (University of Utah), Gregory Voth (University of Chicago), (April2010) "The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials", The Journal of Chemical Physics 132 / 16, 164107. http://dx.doi.org/10.1063/1.3394863
  • Nan-jie Deng, Wei Dai, Ronald Levy (Rutgers, the State University of New Jersey), (2013) "How kinetics within the unfolded state affects protein folding: an anaylsis based on Markov state models and an ultra-long MD trajectory.", Journal of Physical Chemistry B , .
  • Benjamin A. Hall, David Wright (University College, London), Shantenu Jha, Peter V. Coveney, (August2012) "Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity", Biochemistry 51 / 33, 6487-6489. http://dx.doi.org/10.1021/bi300432u