Applications > amber

Publications

Users of this package associated the following 22 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.

  • D. Ofengeim, P. Shi, B. Miao, J. Fan, X. Xia, Yubo Fan (The Methodist Hospital System), M. M. Lipinski, T. Hashimoto, M. Polydoro, J. Yuan, S. T. C. Wong, A. Degterev, (March2012) "Identification of Small Molecule Inhibitors of Neurite Loss Induced by A  peptide using High Content Screening", Journal of Biological Chemistry 287 / 12, 8714-8723. http://dx.doi.org/10.1074/jbc.M111.290957
  • Qiang Shao (DDDC), Yubo Fan (The Methodist Hospital System), Lijiang Yang (Peking University), Yi Qin Gao (Peking University), (March2012) "From protein denaturant to protectant: Comparative molecular dynamics study of alcohol∕protein interactions", The Journal of Chemical Physics 136 / 11, 115101. http://dx.doi.org/10.1063/1.3692801
  • Sakunchai Khumsubdee, Yubo Fan (University of Houston-Downtown), Kevin Burgess, (September2013) "A Comparison between Oxazoline-imidazolinylidene, -imidazolylidine, -benzimidazolylidene Hydrogenation Catalysts", The Journal of Organic Chemistry 78 / 19, 9969-9974. http://dx.doi.org/10.1021/jo4013783
  • Lijiang Yang (Peking University), Yubo Fan (The Methodist Hospital System), Yi Qin Gao (Peking University), (November2011) "Differences of Cations and Anions: Their Hydration, Surface Adsorption, and Impact on Water Dynamics", The Journal of Physical Chemistry B 115 / 43, 12456-12465. http://dx.doi.org/10.1021/jp207652h
  • Q. Wang, Pengzhi Zhang (University of Houston), S. Tripathi, M. S. Cheung, (December2013) "Protein recognition and selection through conformational and mutually induced fit", Proceedings of the National Academy of Sciences 110 / 51, 20545-20550. http://dx.doi.org/10.1073/pnas.1312788110
  • 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
  • Evgeni Penev, Joel Ireta, Joan-Emma Shea, (2008) "Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields", The Journal of Physical Chemistry B 112 / 22, 6872-6877. http://dx.doi.org/10.1021/jp800058f
  • Luca Larini (Rutgers, the State University of New Jersey), Joan-Emma Shea (University of California-Santa Barbara), (2013) "Double Resolution Model for Studying TMAO/Water Effective Interactions", The Journal of Physical Chemistry B 117 / 42, 13268-13277. http://dx.doi.org/10.1021/jp403635g
  • Luca Larini (University of California-Santa Barbara), Megan Murray Gessel, Nichole E. LaPointe, Thanh Do (University of California-Santa Barbara), Michael Bowers (University of California-Santa Barbara), Stuart C. Feinstein, Joan-Emma Shea (University of California-Santa Barbara), (2013) "Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study", Physical Chemistry Chemical Physics 15 / 23, 8916. http://dx.doi.org/10.1039/C3CP00063J
  • Thomas Furlani (SUNY at Buffalo), Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman, (2012) "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience 25 / 7, 918-931. http://dx.doi.org/10.1002/cpe.2871
  • James C. Browne, Thomas Furlani (SUNY at Buffalo), Robert T. McLay, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Amin Ghadersohi, Abani K. Patra, William Barth (University of Texas at Austin), John Hammond, (November2013) "Enabling comprehensive data-driven system management for large computational facilities", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13 Denver, CO, USA , 1-11. http://dx.doi.org/10.1145/2503210.2503230
  • Md Ali (Mount Sinai School of Medicine), Rauf Latif (Mount Sinai School of Medicine), Ramkumarie Baliram (Mount Sinai School of Medicine), Terry Davies (Mount Sinai School of Medicine), Mihaly Mezei (Mount Sinai School of Medicine), (February2013) "MODELLING TSH AND ITS RECEPTOR COMPLEX FOR BINDING AFFINITY", Biophysical Society 57th Annual Meeting Philadelphia , . http://bps2013.conferencespot.org/3416-Pos
  • Yoo-shin Kim, Feng Li, Ren Kong, Yang Bai, King Li, Yubo Fan (University of Houston-Downtown), Brian E. O’Neill, Zheng Li, (August2013) "Multivalency of non-peptide integrin αVβ3 antagonist slows tumor growth", Molecular Pharmaceutics undefined / undefined, 130820125717008. http://dx.doi.org/10.1021/mp400096z
  • Peikai Chen, Y. S. Hung, Tsz-Kwong Man, Ching C. Lau, Yubo Fan (University of Houston-Downtown), (2012) "A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma", 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) Stan Fulton Building, UNLV, Las Vegas, Nevada , 1-6. http://dx.doi.org/10.1109/ICCABS.2012.6182629
  • Peikai Chen, Yubo Fan (University of Houston-Downtown), Tsz-kwong Man, YS Hung, Ching C Lau, (November2013) "A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma", BMC Bioinformatics 14 / Suppl 18, S1. http://dx.doi.org/10.1186/1471-2105-14-S18-S1
  • Liang Gao, Ahmad A. Hammoudi, Fuhai Li, Michael J. Thrall, Philip T. Cagle, Yuanxin Chen, Jian Yang, Xiaofeng Xia, Yubo Fan (The Methodist Hospital System), Yehia Massoud, Zhiyong Wang, Stephen T. C. Wong, (June2012) "Differential diagnosis of lung carcinoma with three-dimensional quantitative molecular vibrational imaging", Journal of Biomedical Optics 17 / 6, 066017. http://dx.doi.org/10.1117/1.JBO.17.6.066017
  • Jiří Šponer, Arnošt Mládek, Naďa Špačková, Xiaohui Cang, Thomas Cheatham (University of Utah), Stefan Grimme, (2013) "Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations", Journal of the American Chemical Society 135 / 26, 9785-9796. http://dx.doi.org/10.1021/ja402525c
  • Vadim Mozhayskiy, Ilias Tagkopoulos (University of California-Davis), (2012) "Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution", BMC Bioinformatics 13 / Suppl 10, S13. http://dx.doi.org/10.1186/1471-2105-13-S10-S13
  • Vadim Mozhayskiy, Ilias Tagkopoulos (University of California-Davis), (2012) "Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation", BMC Bioinformatics 13 / Suppl 10, S10. http://dx.doi.org/10.1186/1471-2105-13-S10-S10
  • Waldemar Debinski, Jian Yang, Jing Fan, Ying Li, Fuhai Li, Peikai Chen, Yubo Fan (University of Houston-Downtown), Xiaofeng Xia, (April2013) "Genome-Wide RNAi Screening Identifies Genes Inhibiting the Migration of Glioblastoma Cells", PLoS ONE 8 / 4, e61915. http://dx.doi.org/10.1371/journal.pone.0061915
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (July2012) "Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling", The Journal of Physical Chemistry B 116 / 29, 8337-8349. http://dx.doi.org/10.1021/jp2097263
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (August2012) "Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25–35) Peptide", Biophysical Journal 103 / 3, 576-586. http://dx.doi.org/10.1016/j.bpj.2012.06.027